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Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875).

Comparative phylogeography has proved useful for investigating biological responses to past climate change and is strongest when combined with extrinsic hypotheses derived from the fossil record or geology. However, the rarity of species with sufficient, spatially explicit fossil evidence restricts the application of this method. Here, we develop an alternative approach in which spatial models of predicted species distributions under serial paleoclimates are compared with a molecular phylogeography, in this case for a snail endemic to the rainforests of North Queensland, Australia. We also compare the phylogeography of the snail to those from several endemic vertebrates and use consilience across all of these approaches to enhance biogeographical inference for this rainforest fauna. The snail mtDNA phylogeography is consistent with predictions from paleoclimate modeling in relation to the location and size of climatic refugia through the late Pleistocene-Holocene and broad patterns of extinction and recolonization. There is general agreement between quantitative estimates of population expansion from sequence data (using likelihood and coalescent methods) vs. distributional modeling. The snail phylogeography represents a composite of both common and idiosyncratic patterns seen among vertebrates, reflecting the geographically finer scale of persistence and subdivision in the snail. In general, this multifaceted approach, combining spatially explicit paleoclimatological models and comparative phylogeography, provides a powerful approach to locating historical refugia and understanding species' responses to them.

Animals↗

Healing with animals in Feira de Santana City, Bahia, Brazil.

This paper discusses the use of animals prescribed as medicines by herbalists from Feira de Santana city in the State of Bahia, Northeastern Brazil. Data were obtained by undergraduates of the Biology course of Feira de Santana State University, who performed open interviews with herbalists at Centro de Abastecimento, the main local market. The medicinally used faunistic resources are echinoderms, arthropods, fish, reptiles, birds and mammals. Folk remedies are administered as teas, syrups or plasters. Respiratory affections predominated and fat was the most common zootherapeutic. It was observed that some of the useful species are in danger of extinction. It is suggested that the rearing of these species in traditional farming systems will allow their conservation, while at the same time they will also results in people's life improvement. Traditional knowledge on folk medicine is to be studied in order to lead to the discovery of new sources of drugs.

Animal Population Groups↗

Bone photovoltaic cell in hall geometry.

Enhancement of photovoltage has been found in bone and its two major constituents when placed in a magnetic field in standard Hall geometry. Infrared light has been used for carrier excitation. From data obtained in this manner, values for the light absorption constant, extinction constant, mass absorption constant, and efficiency have been estimated. All these parameters increase with the increase of magnetic field. A possible explanation for the observed phenomena is presented.

Animals↗

Modelling of predator-prey trophic interactions. Part II: three trophic levels.

A general class of lumped parameter models describing the local dynamics of a tri-trophic chain in a controlled environment is analyzed in detail. The trophic functions characterizing the interactions are defined only by some properties and allow us to treat both prey-dependent and ratio-dependent models in a unified manner. Conditions for existence and stability of extinction and coexistence equilibrium states are determined. Some peculiar aspects of the dynamics of the system depending on the bioecological parameters are presented, with particular attention to bistability situations, limit cycles and chaotic behaviours.

Animals↗

Coexistence of multiple pathogen strains in stochastic epidemic models with density-dependent mortality.

Stochastic differential equations that model an SIS epidemic with multiple pathogen strains are derived from a system of ordinary differential equations. The stochastic model assumes there is demographic variability. The dynamics of the deterministic model are summarized. Then the dynamics of the stochastic model are compared to the deterministic model. In the deterministic model, there can be either disease extinction, competitive exclusion, where only one strain persists, or coexistence, where more than one strain persists. In the stochastic model, all strains are eventually eliminated because the disease-free state is an absorbing state. However, if the population size and the initial number of infected individuals are sufficiently large, it may take a long time until all strains are eliminated. Numerical simulations of the stochastic model show that coexistence cases predicted by the deterministic model are an unlikely occurrence in the stochastic model even for short time periods. In the stochastic model, either disease extinction or competitive exclusion occur. The initial number of infected individuals, the basic reproduction numbers, and other epidemiological parameters are important determinants of the dominant strain in the stochastic epidemic model.

Communicable Diseases↗

Do Eve's alleles live on?

Consider a random sample of genes at a locus, drawn from a population evolving according to the infinitely many, neutral, alleles model. The sample will have a most recent common ancestor gene, which we shall call 'Eve'. The probability distribution, for the number of genes of oldest allelic type in a sample, is known and has a neat form. Rather less is known about the distribution for the number of genes in the sample which are of the same allelic type as Eve possessed. If the latter number is positive, then these genes are automatically of the oldest type in the sample. But Eve may have no non-mutant descendants in the sample; then, the oldest allele will be a mutant arising in a line of descent after Eve. The paper studies the number of non-mutant descendants from Eve, its distribution and moments. It seems that there may be few neat results. In large samples, the proportion of genes of Eve's type has an approximate beta-like density, together with a discrete probability atom at zero, if the mutation rate parameter is low. Extinction of the allele of even the population's common ancestor is possible, but not certain, and bounds are obtained for its probability. Some comments are made about the applications and implications of the results for human mitochondrial DNA.

Alleles↗

Demography of the endangered North Atlantic right whale.

Northern right whales (Eubalaena glacialis) were formerly abundant in the northwestern Atlantic, but by 1900 they had been hunted to near extinction. After the end of commercial whaling the population was thought to be recovering slowly; however, evidence indicates that it has been declining since about 1990 (ref. 1). There are now fewer than 300 individuals, and the species may already be functionally extinct owing to demographic stochasticity or the difficulty of females locating mates in the vast Atlantic Ocean (Allee effect). Using a data set containing over 10,000 sightings of photographically identified individuals we estimated trends in right whale demographic parameters since 1980. Here we construct, using these estimates, matrix population models allowing us to analyse the causes of right whale imperilment. Mortality has increased, especially among mother whales, causing declines in population growth rate, life expectancy and the mean lifetime number of reproductive events between the period 1980-1995. Increased mortality of mother whales can explain the declining population size, suggesting that the population is not doomed to extinction as a result of the Allee effect. An analysis of extinction time shows that demographic stochasticity has only a small effect, but preventing the deaths of only two female right whales per year would increase the population growth rate to replacement level.

Animals↗

Biodiversity conservation: uncertainty in predictions of extinction risk.

Thomas et al. model species-distribution responses to a range of climate-warming scenarios and use a novel application of the species-area relationship to estimate that 15-37% of modelled species in various regions of the world will be committed to extinction by 2050. Although we acknowledge the efforts that they make to measure the uncertainties associated with different climate scenarios, species' dispersal abilities and z values (predictions ranged from 5.6% to 78.6% extinctions), we find that two additional sources of uncertainty may substantially increase the variability in predictions.

Adaptation, Physiological↗

The evolutionary impact of invasive species.

Since the Age of Exploration began, there has been a drastic breaching of biogeographic barriers that previously had isolated the continental biotas for millions of years. We explore the nature of these recent biotic exchanges and their consequences on evolutionary processes. The direct evidence of evolutionary consequences of the biotic rearrangements is of variable quality, but the results of trajectories are becoming clear as the number of studies increases. There are examples of invasive species altering the evolutionary pathway of native species by competitive exclusion, niche displacement, hybridization, introgression, predation, and ultimately extinction. Invaders themselves evolve in response to their interactions with natives, as well as in response to the new abiotic environment. Flexibility in behavior, and mutualistic interactions, can aid in the success of invaders in their new environment.

Animals↗

Plant population dynamics, pollinator foraging, and the selection of self-fertilization.

Many flowering plants rely on pollinators, self-fertilization, or both for reproduction. We model the consequences of these features for plant population dynamics and mating system evolution. Our mating systems-based population dynamics model includes an Allee effect. This often leads to an extinction threshold, defined as a density below which population densities decrease. Reliance on generalist pollinators who primarily visit higher density plant species increases the extinction threshold, whereas autonomous modes of selfing decrease and can eliminate the threshold. Generalist pollinators visiting higher density plant species coupled with autonomous selfing may introduce an effect where populations decreasing in density below the extinction threshold may nonetheless persist through selfing. The extinction threshold and selfing at low density result in populations where individuals adopting a single reproductive strategy exhibit mating systems that depend on population density. The ecological and evolutionary analyses provide a mechanism where prior selfing evolves even though inbreeding depression is greater than one-half. Simultaneous consideration of ecological and evolutionary dynamics confirms unusual features (e.g., evolution into extinction or abrupt increases in population density) implicit in our separate consideration of ecological and evolutionary scenarios. Our analysis has consequences for understanding pollen limitation, reproductive assurance, and the evolution of mating systems.

Animals↗

Pattern of marine mass extinction near the Permian-Triassic boundary in South China.

The Meishan section across the Permian-Triassic boundary in South China is the most thoroughly investigated in the world. A statistical analysis of the occurrences of 162 genera and 333 species confirms a sudden extinction event at 251.4 million years ago, coincident with a dramatic depletion of delta13C(carbonate) and an increase in microspherules.

Animals↗

Interrelationships among biological activity, disulfide bonds, secondary structure, and metal ion binding for a chemically synthesized 34-amino-acid peptide derived from alpha-fetoprotein.

A 34-amino-acid peptide has been chemically synthesized based on a sequence from human alpha-fetoprotein. The purified peptide is active in anti-growth assays when freshly prepared in pH 7.4 buffer at 0.20 g/l, but this peptide slowly becomes inactive. This functional change is proven by mass spectrometry to be triggered by the formation of an intrapeptide disulfide bond between the two cysteine residues on the peptide. Interpeptide cross-linking does not occur. The active and inactive forms of the peptide have almost identical secondary structures as shown by circular dichroism (CD). Zinc ions bind to the active peptide and completely prevents formation of the inactive form. Cobalt(II) ions also bind to the peptide, and the UV-Vis absorption spectrum of the cobalt-peptide complex shows that: (1) a near-UV sulfur-to-metal-ion charge-transfer band had a molar extinction coefficient consistent with two thiolate bonds to Co(II); (2) the lowest-energy visible d-d transition maximum at 659 nm, also, demonstrated that the two cysteine residues are ligands for the metal ion; (3) the d-d molar extinction coefficient showed that the metal ion-ligand complex was in a distorted tetrahedral symmetry. The peptide has two cysteines, and it is speculated that the other two metal ion ligands might be the two histidines. The Zn(II)- and Co(II)-peptide complexes had similar peptide conformations as indicated by their ultraviolet CD spectra, which differed very slightly from that of the free peptide. Surprisingly, the cobalt ions acted in the reverse of the zinc ions in that, instead of stabilizing anti-growth form of the peptide, they catalyzed its loss. Metal ion control of peptide function is a saliently interesting concept. Calcium ions, in the conditions studied, apparently do not bind to the peptide. Trifluoroethanol and temperature (60 degrees C) affected the secondary structure of the peptide, and the peptide was found capable of assuming various conformations in solution. This conformational flexibility may possibly be related to the biological activity of the peptide.

Cations↗

Extending the stochastic two-stage model of carcinogenesis to include self-regulation of the nonmalignant cell population.

One of the challenges of introducing greater biological realism into stochastic models of cancer induction is to find a way to represent the homeostatic control of the normal cell population over its own size without complicating the analysis too much to obtain useful results. Current two-stage models of carcinogenesis typically ignore homeostatic control. Instead, a deterministic growth path is specified for the population of "normal" cells, while the population of "initiated" cells is assumed to grow randomly according to a birth-death process with random immigrations from the normal population. This paper introduces a simple model of homeostatically controlled cell division for mature tissues, in which the size of the nonmalignant population remains essentially constant over time. Growth of the nonmalignant cell population (normal and initiated cells) is restricted by allowing cells to divide only to fill the "openings" left by cells that die or differentiate, thus maintaining the constant size of the nonmalignant cell population. The fundamental technical insight from this model is that random walks, rather than birth-and-death processes, are the appropriate stochastic processes for describing the kinetics of the initiated cell population. Qualitative and analytic results are presented, drawn from the mathematical theories of random walks and diffusion processes, that describe the probability of spontaneous extinction and the size distribution of surviving initiated populations when the death/differentiation rates of normal and initiated cells are known. The constraint that the nonmalignant population size must remain approximately constant leads to much simpler analytic formulas and approximations, flowing directly from random walk theory, than in previous birth-death models.(ABSTRACT TRUNCATED AT 250 WORDS)

Cell Death↗

Sexual selection enhances population extinction in a changing environment.

Animal communication systems (sexual and social communications) may cause an extra selection load on populations because of the cost of the signals. Under environmental deterioration, the cost of signaling must increase, resulting in an evolutionary reduction in the signal if it is maintained by natural selection vs. sexual selection balance. And in turn, the degeneration of the signal tends to reduce the selection load imposed by the cost. But if female preference resides in a population, sexual selection may prevent rapid degeneration of the signal, which is increasingly costly. Hence sexual selection may enhance populational extinction by increasing selection load under environmental changes. This paper evaluates the extra selection load that a communication system suffers when an environment deteriorates or the ecological optimum for a signal changes in the opposite direction to the sexual selection optimum.

Animal Communication↗

Species positions and extinction dynamics in simple food webs.

Recent investigations on the structure of complex networks have provided interesting results for ecologists. Being inspired by these studies, we analyse a well-defined set of small model food webs. The extinction probability caused by internal Lotka-Volterra dynamics is compared to the position of species. Simulations have revealed that some global properties of these food webs (e.g. the homogeneity of connectedness) and the positions of species therein (e.g. interaction pattern) make them prone to modelled biotic extinction caused by population dynamical effects. We found that: (a) homogeneity in the connectedness structure increases the probability of extinction events; (b) in addition to the number of interactions, their orientations also influence the future of species in a web. Since species in characteristic network positions are prone to extinction, results could also be interpreted as describing the properties of preferred states of food webs during community assembly. Our results may contribute to understanding the intimate relationship between pattern and process in ecology.

Animals↗

Choosing appropriate temporal and spatial scales for ecological restoration.

Classic ecological restoration seems tacitly to have taken the Clementsian "balance of nature" paradigm for granted: plant succession terminates in a climax community which remains at equilibrium until exogenously disturbed after which the process of succession is restarted until the climax is reached. Human disturbance is regarded as unnatural and to have commenced in the Western Hemisphere at the time of European incursion. Classic ecological restoration thus has a clear and unambiguous target and may be conceived as aiming to foreshorten the natural processes that would eventually lead to the climax of a given site, which may be determined by its state at "settlement". According to the new "flux of nature" paradigm in ecology a given site has no telos and is constantly changing. Human disturbance is ubiquitous and long-standing, and at certain spatial and temporal scales is "incorporated". Any moment in the past 10,000 years that may be selected as a benchmark for restoration efforts thus appears to be arbitrary. Two prominent conservationists have therefore suggested that the ecological conditions in North America at the Pleistocene-Holocene boundary, prior to the anthropogenic extinction of the Pleistocene megafauna, be the target for ecological restoration. That suggestion explicitly assumes evolutionary temporal scales and continental spatial scales as the appropriate frame of reference for ecological restoration. However, ecological restoration should be framed in ecological spatio-temporal scales, which may be defined temporally in reference to ecological processes such as disturbance regimes and spatially in reference to ecological units such as landscapes, ecosystems, and biological provinces. Ecological spatio-temporal scales are also useful in achieving a scientifically defensible distinction between native and exotic species, which plays so central a role in the practice of ecological restoration and the conservation of biodiversity. Because post-settlement human disturbances have exceeded the limits of such scales, settlement conditions can be justified scientifically as appropriate targets of restoration efforts without recourse to obsolete teleological concepts of equilibria and without ignoring the presence and ecological influence of indigenous peoples.

Animals↗

Assessment of possible ecological risks and hazards of transgenic fish with implications for other sexually reproducing organisms.

Transgenic technology is developing rapidly; however, consumers and environmentalists remain wary of its safety for use in agriculture. Research is needed to ensure the safe use of transgenic technology and thus increase consumer confidence. This goal is best accomplished by using a thorough, unbiased examination of risks associated with agricultural biotechnology. In this paper, we review discussion on risk and extend our approach to predict risk. We also distinguish between the risk and hazard of transgenic organisms in natural environments. We define transgene risk as the probability a transgene will spread into natural conspecific populations and define hazard as the probability of species extinction, displacement, or ecosystem disruption given that the transgene has spread. Our methods primarily address risk relative to two types of hazards: extinction which has a high hazard, and invasion which has an unknown level of hazard, similar to that of an introduced exotic species. Our method of risk assessment is unique in that we concentrate on the six major fitness components of an organism's life cycle to determine if transgenic individuals differ in survival or reproductive capacity from wild type. Our approach then combines estimates of the net fitness parameters into a mathematical model to determine the fate of the transgene and the affected wild population. We also review aspects of fish ecology and behavior that contribute to risk and examine combinations of net fitness parameters which can lead to invasion and extinction hazards. We describe three new ways that a transgene could result in an extinction hazard: (1) when the transgene increases male mating success but reduces daily adult viability, (2) when the transgene increases adult viability but reduces male fertility, and (3) when the transgene increases both male mating success and adult viability but reduces male fertility. The last scenario is predicted to cause rapid extinction, thus it poses an extreme risk. Although we limit our discussion to aquacultural applications, our methods can easily be adapted to other sexually reproducing organisms with suitable adjustments of terminology.

Animals↗

Altruism: its characteristics and evolution.

Altruism is a group phenomenon in which some genes or individuals, which must be presumed to be selfish, benefit others at cost to themselves. The presumption of selfishness and the fact of altruism are reconciled by kin-group selection and by reciprocal altruism. Kin-group selection is clearly visible only in special cases; its role even among social insects may be overestimated; it is probably usually inhibited by competition. However, reciprocal altruism is ubiquitous. All altruism is: (i) potentially reciprocal; (ii) potentially profitable to altruists as well as to recipients; (iii) environmentally determined, usually by position of individuals in group or environmental situations; and (iv) a net-gain lottery. These generalizations are illustrated by four idealized cases; the difficulty of applying them to real cases is illustrated by alarm-calling in groups of birds. Although altruism is a group phenomenon, it evolves by individual selection, by processes equivalent to co-evolutions. Its evolution is: (i) opposed by competition; (ii) costly, complex, and slow, and tending to produce an imprecise flexible altruism rather than a precisely detailed one; and (iii) supplemented by group selection (differential extinction of groups). That altruism in human beings conforms to these generalizations is a good working hypothesis. However, analysis does not "take the altruism out of (human) altruism." Humans do not calculate it, but behave altruistically because they have human altruistic emotions.

Altruism↗