On the dynamical properties of a model of cell differentiation

One of the major challenges in complex systems biology is that of providing a general theoretical framework to describe the phenomena involved in cell differentiation, i.e., the process whereby stem cells, which can develop into different types, become progressively more specialized. The aim of this study is to briefly review a dynamical model of cell differentiation which is able to cover a broad spectrum of experimentally observed phenomena and to present some novel results.     

The extinction context enables extinction performance after a change in context

One experiment with human participants determined the extent to which recovery of extinguished responding with a context switch was due to a failure to retrieve contextually controlled learning, or some other process such as participants learning that context changes signal reversals in the meaning of stimulus-outcome relationships. In a video game, participants learned to suppress mouse clicking in the presence of a stimulus that predicted an attack. Then, that stimulus underwent extinction in a different context (environment within the game). Following extinction, suppression was recovered and then extinguished again during testing in the conditioning context. In a final test, participants that were tested in the context where extinction first took place showed less of a recovery than those tested in a neutral context, but they showed a recovery of suppression nevertheless. A change in context tended to cause a change in the meaning of the stimulus, leading to recovery in both the neutral and extinction contexts. The extinction context attenuated that recovery, perhaps by enabling retrieval of the learning that took place in extinction. Recovery outside an extinction context is due to a failure of the context to enable the learning acquired during extinction, but only in part.     

Scale-free extinction dynamics in spatially structured host-parasitoid systems

Much of the work on extinction events has focused on external perturbations of ecosystems, such as climatic change, or anthropogenic factors. Extinction, however, can also be driven by endogenous factors, such as the ecological interactions between species in an ecosystem. Here we show that endogenously driven extinction events can have a scale-free distribution in simple spatially structured host-parasitoid systems. Due to the properties of this distribution there may be many such simple ecosystems that, although not strictly permanent, persist for arbitrarily long periods of time. We identify a critical phase transition in the parameter space of the host-parasitoid systems, and explain how this is related to the scale-free nature of the extinction process. Based on these results, we conjecture that scale-free extinction processes and critical phase transitions of the type we have found may be a characteristic feature of many spatially structured, multi-species ecosystems in nature. The necessary ingredient appears to be competition between species where the locally inferior type disperses faster in space. If this condition is satisfied then the eventual outcome depends subtly on the strength of local superiority of one species versus the dispersal rate of the other.     

A slowly evolving host moves first in symbiotic interactions

Symbiotic relationships, both parasitic and mutualistic, are ubiquitous in nature. Understanding how these symbioses evolve, from bacteria and their phages to humans and our gut microflora, is crucial in understanding how life operates. Often, symbioses consist of a slowly evolving host species with each host only interacting with its own subpopulation of symbionts. The Red Queen hypothesis describes coevolutionary relationships as constant arms races with each species rushing to evolve an advantage over the other, suggesting that faster evolution is favored. Here, we use a simple game theoretic model of host-symbiont coevolution that includes population structure to show that if the symbionts evolve much faster than the host, the equilibrium distribution is the same as it would be if it were a sequential game where the host moves first against its symbionts. For the slowly evolving host, this will prove to be advantageous in mutualisms and a handicap in antagonisms. The result follows from rapid symbiont adaptation to its host and is robust to changes in the parameters, even generalizing to continuous and multiplayer games. Our findings provide insight into a wide range of symbiotic phenomena and help to unify the field of coevolutionary theory.     

Facets of Pavlovian and operant extinction

Research on extinction is of fundamental importance in both Pavlovian and operant approaches to the experimental analysis of learning. Although these approaches are often motivated by different empirical and theoretical questions, extinction has emerged as a research area in which common themes unite the two approaches. In this review, we focus on some common considerations in the analysis of Pavlovian and operant extinction. These include methodological challenges and interpretational issues in analyzing behavior during and after extinction. We consider the different roles that theory has played in the development of research on extinction in these preparations and conclude with some attention to applications of extinction.     

An assessment of Gallistel's (2012) rationalistic account of extinction phenomena

Gallistel (2012) asserts that animals use rationalistic reasoning (i.e., information theory and Bayesian inference) to make decisions that underlie select extinction phenomena. Rational processes are presumed to lead to evolutionarily optimal behavior. Thus, Gallistel's model is a type of optimality theory. But optimality theory is only a theory, a theory about an ideal organism, and its predictions frequently deviate appreciably from observed behavior of animals in the laboratory and the real world. That is, behavior of animals is often far from optimal, as is evident in many behavioral phenomena. Hence, appeals to optimality theory to explain, rather than illuminate, actual behavior are misguided.     

The controlled assembly of microcosmic communities: the selective extinction hypothesis

Summary Forty communities were assembled through the controlled inoculation of algae, protozoans and a rotifer according to either of 2 distinct introduction schedules. These introduction schedules were constructed such that species reinvaded on average either every 6 or 8 w. Ten of the 20 beakers experiencing each invasion schedule contained 300 ml of media; the remaining beakers in each invasion category contained 100 ml of media. Species richness consistently increased throughout the initial 4 w and 7 w of the experiment for the low and high invasion rate beakers, respectively. The numbers of species in the low rate beakers were uncorrelated with time during the last half of the experiment; however, species richness gradually declined during this period in the high rate beakers. The extinction rate is shown to be disproportionately higher for large organisms in the small microcosms. Such selective extinction is consistent with the MacArthur-Wilson equilibrium model.     

Diversity and extinction patterns of permian brachiopoda of South China

The stratigraphical and geographical distribution of 851 brachiopod species from 216 genera and 65 families in the Permian of South China are analysed. It is revealed that the brachiopod diversity underwent two sharp falls during the Permian. The first occurred at the end of Maokouan, accompaning the widely recognised, extensive regression across the Maokouan‐Wujiapingian boundary. Fifty‐seven species of 29 genera survived this first major extinction event. The second sharp reduction of brachiopod diversity took place in the later Changhsingian, with only 17 Permian‐type brachiopod species of 12 genera straggling into the earliest Triassic. Detailed stratigraphic analysis shows that more than 90% of the Changhsingian brachiopod species disappeared at different levels in the Changhsingian before the widely perceived end‐Permian ‘mass extinction’ occurred. It is also notable that each of the step‐wise diversity reduction events was apparently heterochronous. In view of the evidence from lithologies, faunal components and geochemical analyses, the two sharp falls of Permian brachiopod diversity in South China are considered to be closely related to multiple interactions of an environmental deterioration caused by large‐scale regressions.     

Habitat destruction and the extinction debt revisited: The Allee effect

Habitat destruction, often caused by anthropogenic disturbance, can lead to the extinction of species at an unprecedented rate. It is important, therefore, to consider habitat destruction when assessing population viability. Another factor often ignored in population viability analysis, is the Allee effect that adds to the risk of populations already on the verge of extinction. Understanding the Allee effect on species dynamics and response to habitat destruction has intrinsic value in conservation prioritization. Here, the Allee effect was considered in a multi-species hierarchical competition model. Results showed that species persistence declines dramatically due to the Allee effect, and certain species become more susceptible to habitat destruction than others. Two extinction orders emerged under habitat destruction: either the best competitor becomes extinct first or the best colonizer first. The extinction debt and order, as well as the time lag between habitat destruction and species extinction, were found to be determined by species abundance and the intensity of the Allee effect.     

A dynamical systems perspective on vegetation theory

A dynamical systems perspective is employed to develop a simple conceptual model of vegetation and environment as coupled dynamical systems. The conceptual model characterizes the influence of environment on vegetation, the effect of vegetation on the environment, and the subsequent response of vegetation to the modified environment. Vegetation and environmental dynamics are modeled as trajectories in complementary state spaces, with the trajectories jointly determined by the position of a given site in both spaces. The vegetation and environment state spaces are coupled by the physiological requirements of the component species and the modification of environment by vegetation. From a dynamical systems perspective, current vegetation theory and analyses overemphasize environmental determination of vegetation composition and neglect the effects of vegetation on environment. A dynamical systems perspective is capable of synthesizing previous concepts of vegetation; the continuum and community type concepts are possible consequences of site specific differences in vegetation metabolism and environmental plasticity.I would like to acknowledge the helpful comments and criticisms of Drs G. Cottam, J. D. Aber, T. F. H. Allen, R. P. McIntosh, C. G. Lorimer, and anonymous reviewers.I would like to thank the University of Wisconsin, Madison for a fellowship which supported this research. This paper is dedicated with great respect and gratitude to Professor G. Cottam on the occasion of his retirement from the University of Wisconsin.     

Theoretical approaches for dynamical ordering of biomolecular systems

Background

Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies.

Simple model of recovery dynamics after mass extinction

Biotic recoveries following mass extinctions are characterized by a complex set of dynamics, including the rebuilding of whole ecologies from low-diversity assemblages of survivors and opportunistic species. Three broad classes of diversity dynamics during recovery have been suggested: an immediate linear response, a logistic recovery, and a simple positive feedback pattern of species interaction. Here we present a simple model of recovery which generates these three scenarios via differences in the extent of species interactions, thus capturing the dynamical logic of the recovery pattern. The model results indicate that the lag time to biotic recovery increases significantly as biotic interactions become more important in the recovery process.     

The problem of Dinosaur extinction.Contribution of the study of terminal Cretaceous eggshells from Southeast France

A biostratigraphic sequence based upon dinosaureggshells during the lower and upper Rognacian (upper Cretaceous) in the Aix-en-Provence sedimentary basin (Bouches-du-Rhône, France) has been studied from a morphometric and microstructural viewpoint. Stratigraphic control of eggshell fragment sampling made it possible to follow their evolution throughout the Rognacian. Our results differ from those of certain authors who have worked in this region in that no tendancy toward abnormal eggshell thinness appears at the end of the Cretaceous which could be linked to the problem of dinosaur extinction. Furthermore, we observed no significant increase in the number of bi- or multistratified eggshells («ovum-in-ovo) in the deposits. The microstructural study shows the presence mainly of normal egg-shells belonging to at least three morphotypes.     

The evolution of the Indian Ocean parrots (Psittaciformes): extinction, adaptive radiation and eustacy

Parrots are among the most recognisable and widely distributed of all bird groups occupying major parts of the tropics. The evolution of the genera that are found in and around the Indian Ocean region is particularly interesting as they show a high degree of heterogeneity in distribution and levels of speciation. Here we present a molecular phylogenetic analysis of Indian Ocean parrots, identifying the possible geological and geographical factors that influenced their evolution. We hypothesise that the Indian Ocean islands acted as stepping stones in the radiation of the Old-World parrots, and that sea-level changes may have been an important determinant of current distributions and differences in speciation. A multi-locus phylogeny showing the evolutionary relationships among genera highlights the interesting position of the monotypic Psittrichas, which shares a common ancestor with the geographically distant Coracopsis. An extensive species-level molecular phylogeny indicates a complex pattern of radiation including evidence for colonisation of Africa, Asia and the Indian Ocean islands from Australasia via multiple routes, and of island populations ‘seeding’ continents. Moreover, comparison of estimated divergence dates and sea-level changes points to the latter as a factor in parrot speciation. This is the first study to include the extinct parrot taxa, Mascarinus mascarinus and Psittacula wardi which, respectively, appear closely related to Coracopsis nigra and Psittacula eupatria.     

Late Ordovician extinction of North American and British crinoids

After reaching a diversity peak in the Caradocian, North American Ordovician crinoids underwent a gradual decline to a nadir in the early Ashgillian (Maysvillian). This interval, recording extinction of the Cleiocrinidae, Merocrinidae, Ottawacrinidae, Hybocystitidae, and several lineages of camerate crinoids, was apparently caused by major environmental shifts in seas of eastern North America resulting from a westward-prograding wedge of terrigenous clastics derived from the Taconic Highlands, possibly coupled with a marine transgression in the Maysvillian that allowed colder water slope biofacies to invade the craton. Crinoids suffered a major episode of extinction in the late Ashgillian (late Richmondian/Rawtheyan). This event, preceding the end of the Ordovician by at least one stage or 2 to 4 million years, resulted in extinction of 12 families of crinoids including the Xenocrinidae, Tanaocrinidae, Reteocrinidae, Archaeocrinidae, Anthracocrinidae, Cincinnaticrinidae, Iocrinidae, Anomalocrinidae, Carabocrinidae, Cupulocrinidae, Porocrinidae, and Hybocrinidae. Glacio-eustatic lowering of sea level may have triggered this crisis by partially draining the North American craton, resulting in changes in oceanic circulation, salinity, and temperature. Latest Ordovician (Hirnantian) carbonates of the North American mid-continent region contain pelmatozoan assemblages from which Silurian crinoids radiated. These taxa were largely unaffected by a minor extinction event at the Ordovician/Silurian boundary.     

Diversity and extinction in the Cenozoic history of Caribbean reefs

Occurrences of reef corals are examined at Caribbean fossil localities to determine how biodiversity has changed within the region over the past 50 million years. Analyses of 294 species (66 genera) at 58 fossil localities show that Caribbean generic diversity rose to 44 between 50–22 Ma, ranged from 32–39 between 22–2 Ma, and dropped to 25 afterwards. Regional species diversity was high at 40–36 Ma, 28–22 Ma, and 5–2 Ma. Origination rates were elevated throughout each high diversity interval, but extinction was concentrated near the end of each interval. Regional highs of origination and extinction, therefore, differed in timing and duration, causing the observed regional diversity increases during the three remarkably long intervals of turnover. Highs of generic origination decreased in magnitude as immigration from the Mediterranean ceased, but speciation highs increased in association with emergence of the Central American isthmus. Peaks of extinction coincided with regional changes in climate and oceanic circulation. Maximum species diversities within assemblages increased to 40–60 between 50–36 Ma, and have remained relatively constant ever since. Assemblage compositions differed among localities having similar ages and environments, suggesting that the timing and pattern of turnover varied across the region. Stable diversities but variable compositions within assemblages suggest that dispersal and recruitment influenced the pattern of faunal change during turnover. Accepted: 22 August 1999     

Population extinction risks of three Neotropical small mammal species

The population persistence and extinction probabilities of three small mammal species were analyzed by estimating growth and extinction properties obtained from 10 years of live-trapping data at two different habitat types in semiarid Chile. We used a stochastic formulation with an exponential growth model known as a Wiener-drift process, out of which growth and extinction quantities were estimated. The rodent Phyllotis darwini showed the lowest rates of growth, and the lowest infinitesimal variances, whereas the opposite trend was found for the rodent Akodonolivaceus. The marsupial Thylamys elegans showed intermediate values for growth rates and infinitesimal variances. The rodent P. darwini showed the lowest extinction risk in the study site. We also detected spatial differences between mesic and xeric habitats in the growth rates of P. darwini and T. elegans, and in the extinction risks of the three species studied. Although the population growth of these three species can be approximated by purely stochastic processes, the introduction of density dependence through autoregressive log-linear models reduced the extinction times of all species analyzed. Received: 16 May 1997 / Accepted: 22 January 1998     

The pineal gland of nocturnal mammals

Summary In the pineal gland of the pipistrelle bat two different populations of pinealocytes and glial cells were observed electron microscopically. The pinealocytes of populations I and II differ in their content of metabolically active cell organelles. In the pinealocytes of population I, granular vesicles originating from the Golgi apparatus were found in the perikaryon and especially in the endings of the pinealocyte processes. Granular vesicles appeared to be more numerous in hibernating nulliparous females. The pinealocytes of population II are characterized by the presence of small cytoplasmic vacuoles, probably originating from cisternae of the granular endoplasmic reticulum and containing flocculent material of moderate electron density. The classification of the pinealocytes belonging to population II is discussed.This collaboration was initiated with the aid of an SRC European short visit grant to P.A.R.The study was supported by the Foundation for Medical Research, the Netherlands (FUNGO, 13-35-33)     

Plant extinction in New Caledonia: protection of sclerophyll forests urgently needed

The sclerophyll forests which once extended over the lowlands of the west coast of New Caledonia are now reduced to small fragments representing about 2% (10 000 ha) of their original area. Much of the remaining forests are degraded. Threats to sclerophyll forests come from land clearance, grazing by cattle or deer, and fire. In sclerophyll forests, 223 endemic phanerogam species occur and 59 of these are specific to this forest type. Several of the 59 specific species are known only from a few plants at a single locality and are critically endangered. Pittosporum tanianum sp. nov. became extinct shortly after its discovery in 1988, and becomes the first documented plant extinction in New Caledonia. A further 15 species of New Caledonian plants, not recorded for several decades, are discussed, and it is concluded that between 4 and 9 of them may be extinct. The existing reserves containing sclerophyll forests are inadequate to protect the remaining biodiversity of the forests. Four immediate steps needed to protect sclerophyll forests are (i) restoration of Leprédour Island; (ii) purchase and restoration of selected privately owned forests; (iii) management of publicly owned forest near Népoui; and (iv) ex situ conservation of certain species.     

Asymptotic rates of growth of the extinction probability of a mutant gene

We prove that a result of Haldane (1927) that relates the asymptotic behaviour of the extinction probability of a slightly supercritical Poisson branching process to the mean number of offspring is true for a general Bienaymé-Galton-Watson branching process, provided that the second derivatives of the probability-generating functions converge uniformly to a non-zero limit. We show also by examples that such a result is true more widely than our proof suggests and exhibit some counter-examples.Research supported by NSERC