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PubMed2004

Can extinction rates be estimated without fossils?

There is considerable interest in the possibility of using molecular phylogenies to estimate extinction rates. The present study aims at assessing the statistical performance of the birth-death model fitting approach to estimate speciation and extinction rates by comparison to the approach considering fossil data. A simulation-based approach was used. The diversification of a large number of lineages was simulated under a wide range of speciation and extinction rate values. The estimators obtained with fossils performed better than those without fossils. In the absence of fossils (e.g. with a molecular phylogeny), the speciation rate was correctly estimated in a wide range of situations; the bias of the corresponding estimator was close to zero for the largest trees. However, this estimator was substantially biased when the simulated extinction rate was high. On the other hand the estimator of extinction rate was biased in a wide range of situations. Surprisingly, this bias was lesser with medium-sized trees. Some recommendations for interpreting results from a diversification analysis are given.

Animals↗

PubMed2006

Responses of canine oocytes to in vitro maturation and in vitro fertilization outcome.

The potential benefits of assisted reproduction techniques, such as in vitro maturation (IVM) and in vitro fertilization (IVF) in canids, are linked to the protection and saving of species threatened by extinction due to worldwide habitat destruction and pollution. In both domestic and wild species, these technologies will form the basis for the next leap in reproductive performance by improving fertility rates in valuable middle-aged females, by improving pregnancy rate in infertile or sub-fertile populations and by rescuing biological material to replenish populations of endangered species. In vitro techniques are supposed to answer the reproductive questions of canids, to introduce new methods for contraception and to compete with artificial insemination (AI) as the major or predominant method of embryo production, oocyte- and embryo cryopreservation and cloning. The causes affecting in vitro meiosis of dog oocytes are likely to be diverse. Incomplete understanding of the events associated with oocyte developmental competence are imputed to species reproductive physiology, medium composition and source of ovarian oocyte population used for in vitro maturation. This review addresses some issues on the current state of in vitro maturation and in vitro fertilization of canine oocytes.

Animals↗

PubMed2005

Astronomical pacing of methane release in the Early Jurassic period.

A pronounced negative carbon-isotope (delta13C) excursion of approximately 5-7 per thousand (refs 1-7) indicates the occurrence of a significant perturbation to the global carbon cycle during the Early Jurassic period (early Toarcian age, approximately 183 million years ago). The rapid release of 12C-enriched biogenic methane as a result of continental-shelf methane hydrate dissociation has been put forward as a possible explanation for this observation. Here we report high-resolution organic carbon-isotope data from well-preserved mudrocks in Yorkshire, UK, which demonstrate that the carbon-isotope excursion occurred in three abrupt stages, each showing a shift of -2 per thousand to -3 per thousand. Spectral analysis of these carbon-isotope measurements and of high-resolution carbonate abundance data reveals a regular cyclicity. We interpret these results as providing strong evidence that methane release proceeded in three rapid pulses and that these pulses were controlled by astronomically forced changes in climate, superimposed upon longer-term global warming. We also find that the first two pulses of methane release each coincided with the extinction of a large proportion of marine species.

Animals↗

PubMed1983

Multiple origins of life.

There is some indication that life may have originated readily under primitive earth conditions. If there were multiple origins of life, the result could have been a polyphyletic biota today. Using simple stochastic models for diversification and extinction, we conclude: (i) the probability of survival of life is low unless there are multiple origins, and (ii) given survival of life and given as many as 10 independent origins of life, the odds are that all but one would have gone extinct, yielding the monophyletic biota we have now. The fact of the survival of our particular form of life does not imply that it was unique or superior.

Biological Evolution↗

PubMed2003

Cenozoic bolide impacts and biotic change in North American mammals.

North American mammals experienced a major mass extinction at the Cretaceous/Tertiary (K/T) boundary that is tied unambiguously to the Chicxulub impact event. Immediately afterwards, there was an immense adaptive radiation that greatly expanded taxonomic diversity and the range of body sizes and ecological strategies. However, ties between later, Cenozoic impact events and specific episodes in mammalian evolution cannot be demonstrated. A time series of maximum known crater sizes within 1.0-million-year-long temporal bins is shown not to cross-correlate with five separate measures of taxonomic turnover rate, one measure of change in relative taxonomic composition, and four measures of change in body mass distributions. The lack of correlation persists even after excluding the volatile Paleocene mammalian data, adding dummy data to represent intervals without known craters, or lagging the time series against each other for up to 5 million years. Furthermore, the data fail to support broad-brush correspondences between ages of major (>20 km in diameter) craters and the timing of five key, post-K/T biotic transitions, including medium-sized extinction episodes during the late Paleocene and latest Miocene. The results challenge the idea that extraterrestrial impacts drive all, most, or even many extinction and radiation episodes in terrestrial organisms, and add to other evidence that natural, long-term biotic changes are often independent of changes in the physical environment.

Animals↗

PubMed2000

Temporally explicit habitat ecology and the coexistence of species.

Habitats may have dynamics that exist independently of the population densities of species occupying the habitat. For example, ephemeral habitat patches may disappear regardless of whether a particular species is present or not. Such habitat dynamics are frequently modelled by ignoring age-related variation in patch turnover rates. This can be thought of as a temporally implicit approach. An alternative, temporally explicit approach involves using age-structured models in order to describe variations in habitat dynamics. Simple models of coexistence between competing species show that temporally implicit models may be misleading where there is age-related variation in patch dynamics. Changing the shape of the patch survivorship function but not the average patch survivorship can result in mutual extinction, monocultures or coexistence of an inferior and a superior competitor. An explicit treatment of habitat demography may therefore offer improved predictive models and alternative landscape management strategies.

Animals↗

PubMed2006

Coevolution of slow-fast populations: evolutionary sliding, evolutionary pseudo-equilibria and complex Red Queen dynamics.

We study the interplay of ecological and evolutionary dynamics in communities composed of populations with contrasting time-scales. In such communities, genetic variation of individual traits can cause population transitions between stationary and cyclic ecological regimes, hence abrupt variations in fitness. Such abrupt variations raise ridges in the adaptive landscape, where the populations are poised between equilibrium and cyclic coexistence and along which evolutionary trajectories can remain sliding for long times or halt at special points called evolutionary pseudo-equilibria. These novel phenomena should be generic to all systems in which ecological interactions cause fitness to vary discontinuously. They are demonstrated by the analysis of a predator-prey community, with one adaptive trait for each population. The eco-evolutionary dynamics of the system show a number of other distinctive features, including evolutionary extinction and two forms of Red Queen dynamics. One of them is characterized by intermittent bouts of cyclic oscillations of the two populations.

Adaptation, Physiological↗

PubMed1992

Population dynamics and control of Triatoma infestans.

Analysis of field populations of Triatoma infestans (Hemiptera: Reduviidae), after a 3-year study, shows that population growth rate is affected by both density-dependent and density-independent mortality. Although an equilibrium exists, apparently as a consequence of a density dependent-mechanism, population density fluctuates throughout the year because of the effect of monthly mean minimum temperature as a density-independent source of mortality. Simulation studies based on Moran curves shows that high population densities have an approximately constant extinction probability (around 0.20), independently of the season the population starts growing. However, at very low population densities, the extinction probability depends strongly on the season when the population begins to grow. Very low density populations beginning in winter or autumn have the highest extinction probability. The outcome of the simulation studies coincides with results observed in field populations affected by insecticide application at different seasons.

Animals↗

PubMed2006

Fragments as islands: a synthesis of faunal responses to habitat patchiness.

Scientific interest in the impact of habitat fragmentation on biodiversity is increasing, but our understanding of fragmentation is clouded by a lack of appreciation for fundamental similarities and differences across studies representing a wide range of taxa and landscape types. In an effort to synthesize data describing ecological responses of animals to fragmentation across two classes of independent variables (taxonomic group and landscape), we sampled 148 studies offive major faunal groups from the primary literature and analyzed data on 13 variables extracted from those studies. We focused our analyses on three classes of dependent variables (effects of area and isolation on species richness, z values, and nestedness and species composition). Area ranged over more orders of magnitude than isolation and tended to explain more variation in species richness than isolation. There were few matrix or taxon effects on the patterns we investigated, although we did find that sky islands tended to manifest isolation effects on both species richness and nestedness more frequently than other patch types. Sky islands may offer insight into the future of habitat patches fragmented by contemporary habitat loss, and because they show a stronger effect of isolation than other patch types, we suggest that isolation will play an increasing role in the biology of habitat fragments. We use multiple lines of evidence to suggest that our understanding of the role of isolation on community assembly in fragmented landscapes is inadequate. Finally, our observation that consistent taxonomic differences in community patterns were minimal suggests that conservation actions intended to mitigate the negative effects of extinction may have far-reaching effects across taxonomic groups.

Animals↗

PubMed1980

Some characteristics of a new multiple-channel photometer for through-the-plate reading of microplates to be used in enzyme-linked immunosorbent assay.

The performance of a prototype of a now commercially available multiple-channel photometer for high-speed reading of microplates to be used in the enzyme-linked immunosorbent assay was evaluated. For this purpose the extinction of a stable test liquid dispensed in flat-bottomed polystyrene microplates was measured, varying the test volume and the optical density. From the results obtained for dilutions of a single, biolgoically inactive material we concluded that the photometric inaccuracy is negligible when performing enzyme-linked immunosorbent assay with biologically active samples.

Enzyme-Linked Immunosorbent Assay↗

PubMed2006

Global patterns of geographic range size in birds.

Large-scale patterns of spatial variation in species geographic range size are central to many fundamental questions in macroecology and conservation biology. However, the global nature of these patterns has remained contentious, since previous studies have been geographically restricted and/or based on small taxonomic groups. Here, using a database on the breeding distributions of birds, we report the first (to our knowledge) global maps of variation in species range sizes for an entire taxonomic class. We show that range area does not follow a simple latitudinal pattern. Instead, the smallest range areas are attained on islands, in mountainous areas, and largely in the southern hemisphere. In contrast, bird species richness peaks around the equator, and towards higher latitudes. Despite these profoundly different latitudinal patterns, spatially explicit models reveal a weak tendency for areas with high species richness to house species with significantly smaller median range area. Taken together, these results show that for birds many spatial patterns in range size described in geographically restricted analyses do not reflect global rules. It remains to be discovered whether global patterns in geographic range size are best interpreted in terms of geographical variation in species assemblage packing, or in the rates of speciation, extinction, and dispersal that ultimately underlie biodiversity.

Animals↗

PubMed1970

The chemistry of vitamin B 12. The co-ordination of biologically important molecules.

The following equilibrium constants (given as logK in units of m(-1)) were determined for the substitution of co-ordinated H(2)O in aquocobalamin by glycine (bound through N) 5.8, cysteine (bound through S) 6.0 or 8.3, depending on the value chosen for the pK of the thiol group, and phenolate 2.9. The spectrum of the phenolate cobalamin shows an additional intense absorption band at 468nm with a molar extinction coefficient of 1.1x10(4), which is assigned to a charge transfer from the phenolate to the cobalt ion. Equilibrium constants have also been determined for the equilibria between adenylcobamide cyanide and CN(-), HO(-) and H(+), which show that the adenine is more easily displaced by CN(-) and HO(-) than is 5,6-dimethylbenziminazole in vitamin B(12), but can be protonated by acid while still remaining co-ordinated to the cobalt. It is shown that in the binding of corrinoids to proteins and polypeptides the formation of hydrogen bonds is far more important than co-ordination by the metal.

Adenine↗

PubMed2006

Conservation of genes and culture: historical and contemporary issues.

The paper examines the reasons for and consequences of lost domestic animal biodiversity. The origin of domestic poultry and livestock diversity is reviewed from the first center of domestication in the Middle East during the Neolithic Revolution. Accompanied by domestic animals and birds, mankind spread worldwide over the last 12,000 yr, thereby increasing domestic animal biodiversity via adaptation to many environmental challenges, resulting in about 6,000 breeds within only a small number of species used for food. During the last 50 yr of the 20th century, about 20% of these livestock and poultry breeds have become extinct, and the remainder is at risk. This erosion of unique biodiversity is due to changes in farm practices developed in the West that involve mono-breed, intensive farming systems that are unsustainable. The close symbiotic relationship of Homo sapiens and domestic animals and birds over millennia is changing, resulting in a lost understanding of sustainability among urban communities. The single-minded focus on profit is resulting in the loss of the historic European and Western culture based on Judeo-Christian values. Respect for biological boundaries, community, and quality of life are disappearing in Western society. Concurrently, farming is now only a business. The principal decision makers are no longer farmers but business executives, who are remote from the farm. The emphasis on cheap food is the principal driver that leads to increased competition and unsustainable practices. Farmers as well as their breeds are disappearing. The advent of gene technology and transgenic livestock is reviewed with the prospect of extensive manipulation of animal form and function and abuse of genotypes as animals are redesigned, suffer, and lose all dignity. By handling its animals in this manner, high Western civilization is losing its culture and values and becoming simply the top animal species by using its power selfishly. The case is presented that the extinction of animals indicates an urgent need to conserve historic Western culture before it, too, is lost.

Animals↗

PubMed1993

Psychoneuroimmunology: conditioning and stress.

The acquisition and extinction of the conditioned suppression or enhancement of one or another parameter of antigen-specific and nonspecific defense system responses have been documented in different species under a variety of experimental conditions. Similarly, stressful stimulation influences antigen-specific as well as nonspecific reactions. Moreover, both conditioning and stressful stimulation exert biologically meaningful effects in the sense that they can alter the development and/or progression of what are presumed to be immunologically mediated pathophysiologic processes. These are highly reproducible phenomena that illustrate a functional relationship between the brain and the immune system. However, the extent to which one can generalize from one stressor to another or from one parameter of immunologic reactivity to another is limited. Few generalizations are possible because the direction and/or magnitude of the effects of conditioning and "stress" in modulating immune responses clearly depend on the quality and quantity of the behavioral interventions, the quality and quantity of antigenic stimulation, the temporal relationship between behavioral and antigenic stimulation, the nature of the immune response and the immune compartment in which it is measured, the time of sampling, a variety of host factors (e.g. species, strain, age, sex), and interactions among these several variables. It seems reasonable to assume that the immunologic effects of behaviorally induced neural and endocrine responses depend on (interact with) the concurrent immunologic events upon which they are superimposed. Conversely, the efficacy of immunologic defense mechanisms seems to depend on the neuroendocrine environment on which they are superimposed. We seek to determine when and what immunologic (or neuroendocrine) responses could be affected by what neuroendocrine (or immunologic) circumstances. We therefore need studies that provide a parametric analysis of the stimulus conditions, the neuroendocrine and/or immunologic state upon which they are superimposed, and the responses that are being sampled. The neural or neuroendocrine pathways involved in the behavioral alteration of immune responses are not yet known. Both conditioning and stressor-induced effects have been hypothesized to result from the action of adrenocortical steroids, opioids, and catecholamines, among others. Indeed, all of these have been implicated in the mediation of some immunologic effects observed under some experimental conditions. We assume that different conditioning and stressful environmental circumstances induce different constellations of neuroendocrine responses that constitute the milieu within which ongoing immunologic reactions and the response to immunologic signals occur.(ABSTRACT TRUNCATED AT 400 WORDS)

Conditioning, Psychological↗

PubMed1986

Persistence in population models with demographic fluctuations.

A persistence and extinction theory is developed through analytical studies of deterministic population models. Under hypotheses that require demographic parameters to fluctuate temporally, the populations may or may not oscillate. Extinction, when it occurs, is asymptotic. An hierarchy of persistence criteria, based upon fluctuations measured by time average means, is derived. In some situations a threshold value is found to separate persistent population models from those that tend to extinction. Application of the persistence-extinction theory is to the problem of assessing effects of a toxic substance on a population when toxicant inputs to the environment and to resources are oscillatory.

Demography↗

PubMed2005

Rock-scissors-paper game in a chaotic flow: the effect of dispersion on the cyclic competition of microorganisms.

Laboratory experiments and numerical simulations have shown that the outcome of cyclic competition is significantly affected by the spatial distribution of the competitors. Short-range interaction and limited dispersion allows for coexistence of competing species that cannot coexist in a well-mixed environment. In order to elucidate the mechanisms that destroy species diversity we study the intermediate situation of imperfect mixing, typical in aquatic media, in a model of cyclic competition between toxin producing, sensitive and resistant phenotypes. It is found, that chaotic mixing, by changing the character of the spatial distribution, induces coherent oscillations in the populations. The magnitude of the oscillations increases with the strength of mixing, leading to the extinction of some species beyond a critical mixing rate. When mixing is non-uniform in space, coexistence can be sustained at much stronger mixing by the formation of partially isolated regions, that prevent global extinction. The heterogeneity of mixing may enable toxin producing and sensitive strains to coexist for very long time at strong mixing.

Animals↗

PubMed1997

Prey dominance in discrete predator-prey systems with a prey refuge.

The effects of a prey refuge in a multiprey discrete system with predation is studied. We demonstrate the stable coexistence of species that would otherwise exclude each other without a prey refuge. With a prey refuge, we show that an endangered prey not only recovers from the brink of extinction, but also dominates the system. We invent notions of dominance that guarantee the extinction of all the dominated prey in the system. With the extermination of most of its prey, the predator either coexists with the dominant prey or is driven to extinction. By using a precise mathematical definition, we obtain that a prey with a sufficiently high carrying capacity persists in a predator-prey system with a prey refuge.

Animals↗

PubMed2003

Rapid body size decline in Alaskan Pleistocene horses before extinction.

About 70% of North American large mammal species were lost at the end of the Pleistocene epoch. The causes of this extinction--the role of humans versus that of climate--have been the focus of much controversy. Horses have figured centrally in that debate, because equid species dominated North American late Pleistocene faunas in terms of abundance, geographical distribution, and species variety, yet none survived into the Holocene epoch. The timing of these equid regional extinctions and accompanying evolutionary changes are poorly known. In an attempt to document better the decline and demise of two Alaskan Pleistocene equids, I selected a large number of fossils from the latest Pleistocene for radiocarbon dating. Here I show that horses underwent a rapid decline in body size before extinction, and I propose that the size decline and subsequent regional extinction at 12,500 radiocarbon years before present are best attributed to a coincident climatic/vegetational shift. The present data do not support human overkill and several other proposed extinction causes, and also show that large mammal species responded somewhat individualistically to climate changes at the end of the Pleistocene.

Alaska↗