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PubMed2003

Evolution, climatic change and species boundaries: perspectives from tracing Lemmiscus curtatus populations through time and space.

To provide empirical evidence of species boundaries and the role of climatic change in affecting evolution, we documented evolution of the sagebrush vole, Lemmiscus curtatus, through hundreds of thousands of years by following populations from the middle Pleistocene to the present. We found that: (i) extant representatives of the species culminate a morphological transition that was initiated within an unusually arid and warm interglacial period, perhaps related to the shift from glacial-interglacial cycles dominated by a 41,000 year periodicity to those dominated by a 100,000 year rhythm; and (ii) sympatry of extant and extinct morphotypes persisted for more than 800,000 years. This exceptionally detailed tracing of extinct populations into extant ones suggests that species such as the one we studied are real entities in space, that their boundaries become fuzzy (although potentially diagnosable) through time and that unusual climatic warming may initiate significant evolutionary change manifested at the morphological level.

Animals↗

PubMed2004

Tolerance of pollination networks to species extinctions.

Mutually beneficial interactions between flowering plants and animal pollinators represent a critical 'ecosystem service' under threat of anthropogenic extinction. We explored probable patterns of extinction in two large networks of plants and flower visitors by simulating the removal of pollinators and consequent loss of the plants that depend upon them for reproduction. For each network, we removed pollinators at random, systematically from least-linked (most specialized) to most-linked (most generalized), and systematically from most- to least-linked. Plant species diversity declined most rapidly with preferential removal of the most-linked pollinators, but declines were no worse than linear. This relative tolerance to extinction derives from redundancy in pollinators per plant and from nested topology of the networks. Tolerance in pollination networks contrasts with catastrophic declines reported from standard food webs. The discrepancy may be a result of the method used: previous studies removed species from multiple trophic levels based only on their linkage, whereas our preferential removal of pollinators reflects their greater risk of extinction relative to that of plants. In both pollination networks, the most-linked pollinators were bumble-bees and some solitary bees. These animals should receive special attention in efforts to conserve temperate pollination systems.

Animals↗

PubMed2001

Extinctions in the random replicator model.

The statistical properties of an ecosystem composed of species interacting via pairwise, random interactions and deterministic, concentration limiting self-interactions are studied analytically with tools of equilibrium statistical mechanics of disordered systems. Emphasis is given to the effects of externally induced extinction of a fixed fraction of species at the outset of the evolutionary process. The manner the ecosystem copes with the initial extinction event depends on the degree of competition among the species as well as on the strength of that event. For instance, in the regime of high competition the ecosystem diversity, given by the fraction of surviving species, is practically insensitive to the strength of the initial extinction provided it is not too large, while in the less competitive regime the diversity decreases linearly with the size of the event. In the case of large extinction events we find that no further biotic extinctions take place and, furthermore, that rare species become very unlikely to be found in the ecosystem at equilibrium. In addition, we show that the reciprocal of the Edwards-Anderson order parameter yields a good measure of the diversity of the model ecosystem.

Animals↗

PubMed2002

Escalation and extinction selectivity: morphology versus isotopic reconstruction of bivalve metabolism.

Studies that have tested and failed to support the hypothesis that escalated species (e.g., those with predation-resistant adaptations) are more susceptible to elimination during mass extinctions have concentrated on the distribution and degree of morphological defenses in molluscan species. This morphological approach to determining level of escalation in bivalves may be oversimplified because it does not account for metabolic rate, which is an important measure of escalation that is less readily accessible for fossils. Shell growth rates in living bivalves are positively correlated with metabolic rate and thus are potential indicators of level of escalation. To evaluate this approach, we used oxygen isotopes to reconstruct shell growth rates for two bivalve species (Macrocallista marylandica and Glossus markoei) from Miocene-aged sediments of Maryland. Although both species are classified as non-escalated based on morphology, the isotopic data indicate that M. marylandica was a faster-growing species with a higher metabolic rate and G. markoei was a slower-growing species with a lower metabolic rate. Based on these results, we predict that some morphologically non-escalated species in previous tests of extinction selectivity should be reclassified as escalated because of their fast shell growth rates (i.e., high metabolic rates). Studies that evaluate the level of escalation of a fauna should take into account the energetic physiology of taxa to avoid misleading results.

Animals↗

PubMed2002

A comprehensive model of mutations affecting fitness and inferences for Arabidopsis thaliana.

As the ultimate source of genetic variation, spontaneous mutation is essential to evolutionary change. Theoretical studies over several decades have revealed the dependence of evolutionary consequences of mutation on specific mutational properties, including genomic mutation rates, U, and the effects of newly arising mutations on individual fitness, s. The recent resurgence of empirical effort to infer these properties for diverse organisms has not achieved consensus. Estimates, which have been obtained by methods that assume mutations are unidirectional in their effects on fitness, are imprecise. Both because a general approach must allow for occurrence of fitness-enhancing mutations, even if these are rare, and because recent evidence demands it, we present a new method for inferring mutational parameters. For the distribution of mutational effects, we retain Keightley's assumption of the gamma distribution, to take advantage of the flexibility of its shape. Because the conventional gamma is one sided, restricting it to unidirectional effects, we include an additional parameter, rho, as an amount it is displaced from zero. Estimation is accomplished by Markov chain Monte Carlo maximum likelihood. Through a limited set of simulations, we verify the accuracy of this approach. We apply it to analyze data on two reproductive fitness components from a 17-generation mutation-accumulation study of a Columbia accession of Arabidopsis thaliana in which 40 lines sampled in three generations were assayed simultaneously. For these traits, U approximately/= 0.1-0.2, with distributions of mutational effects broadly spanning zero, such that roughly half the mutations reduce reproductive fitness. One evolutionary consequence of these results is lower extinction risks of small populations of A. thaliana than expected from the process of mutational meltdown. A comprehensive view of the evolutionary consequences of mutation will depend on quantitatively accounting for fitness-enhancing, as well as fitness-reducing, mutations.

Algorithms↗

PubMed1997

Theoretical considerations on the nature of the pineal 'ageing clock'.

The models developed in our laboratory demonstrate that ageing initiates and progresses in the pineal gland. However, the ageing postponing effects of pineal grafting into older recipients cannot be explained by a simple maintenance and/or normalization of the night melatonin synthesis and release. We propose here that the pineal gland monitors and regulates, via its control of neuroendocrine function, the maintenance of 'self-identity' and the capacity of the immune system to recognize and react against any noxious, endogenous or exogenous agent. Senescence is characterized by the extinction of this central pineal function. The progressive decline of the self-recognition capacity distinguishes the typical diseases of ageing expressed as emergence of peripheral desynchronization and autoimmune, anaplastic, neoplastic and degenerative processes. Our approaches aim at a prevention and/or restoration of central pineal functions.

Aging↗

PubMed1981

Characterization of a new type of ferredoxin from Desulfovibrio africanus.

A new ferredoxin designated ferredoxin III has been isolated from Desulfovibrio africanus grown on media high in iron. Native ferredoxin III is a dimer constituted by two identical subunits of approx. 7500. It is distinguished from the two other ferredoxins (I and II) isolated from this microorganism by its amino acids composition, N-terminal sequence, spectral properties and iron-sulfur content. The amino acid composition of D. africanus ferredoxin III is typical of ferredoxins with an excess of acidic over basic residues and the absence of histidine and arginine residues. The absorption spectrum of ferredoxin III exhibits two maxima, at 408 nm (epsilon = 58.5 . 10(3) M-1 . cm-1) and 285 nm (epsilon = 82 . 10(3) M-1 . cm-1), with a shoulder at 305 nm (epsilon = 75 . 10(3) M-1 . cm-1). Its A408/A285 absorbance ratio is 0.78. Ferredoxin III contains approx. 12--13 atoms each of iron and labile sulfur. This is in agreement with the high value of the extinction coefficient at 408 nm, which is slightly higher than 3-fold that of one [4Fe-4S] cluster. However, the number of cysteine residues of the protein (six residues), which is about the half that of iron atoms, is indicative of the presence of a new type of iron-sulfur cluster in ferredoxin III. The protein is unstable in a low ionic strength environment; the addition of neutral salts stabilizes the protein conformation. The data on the biological activity of ferredoxin III as compared to the two other ferredoxins from D. africanus show that the three iron-sulfur proteins function with equal effectiveness as electron carrier in the phosphoroclastic reaction and the H2-sulfite reductase system.

Amino Acid Sequence↗

PubMed2004

The comparative method in conservation biology.

The phylogenetic comparative approach is a statistical method for analyzing correlations between traits across species. Whilst it has revolutionized evolutionary biology, can it work for conservation biology? Although it is correlative, advocates of the comparative method hope that it will reveal general mechanisms in conservation, provide shortcuts for prioritizing conservation research, and enable us to predict which species will experience (or create) problems in the future. Here, we ask whether these stated management goals are being achieved. We conclude that comparative methods are stimulating research into the ecological mechanisms underlying conservation, and are providing information for preemptive screening of problem species. But comparative analyses of extinction risk to date have tended to be too broad in scope to provide shortcuts to conserving particular endangered species. Correlates of vulnerability to conservation problems are often taxon, region and threat specific, so models must be narrowly focused to be of maximum practical use.

Journal Article↗

PubMed1997

Damage proneness induced by genomic DNA demethylation in mammalian cells cultivated in vitro.

Variations in the genomic DNA methylation level have been shown to be an epigenetic inheritable modification affecting, among other targets, the sister chromatid exchange (SCE) rate in mammalian cells in vitro. The inheritable increase in SCE rate in affected cell populations appears as a puzzling phenomenon in view of the well established relation between SCE and both mutagenesis and carcinogenesis. In the present work we demonstrate that, in a treated cell population, demethylation could be responsible for the inheritable induction of damage proneness affecting both damage induction and repair. Normal and ethionine or azacytidine treated Chinese hamster ovary cells, subclone K1 (CHO-K1), were challenged with UV light (UV) or mitomycin-C (MMC) at different times from the demethylating treatment. The SCE rate was measured with two main objects in view: (i) the induction of synergism or additivity in combined treatments, where mutagen (UV or MMC) pulse is supplied from 0 to 48 h after the end of the demethylating treatment; and (ii) the pattern of damage extinction, for the duration of up to six cell cycles after the end of the combined (demethylating agent + mutagen) treatment. Results indicate both a synergism in SCE induction by mutagens in demethylated cells even if supplied up to four cell cycles after the end of the demethylation treatment and a delay in recovery of induced damage, compared with normally methylated cells. These data are discussed in the light of the supposed mechanism of SCE increase and of the possible biological significance in terms of mutagenesis and carcinogenesis.

Animals↗

PubMed1984

Chemical and biological evolution in space.

Astronomical infrared spectra are used to confirm the existence of complex organic molecules produced by ultraviolet photoprocessing of interstellar grain mantles. This material is shown to be the major component of the interstellar grains between the sun and the galactic center and, by inference, constitutes more than 10 million solar masses--or close to one part in a thousand of the entire mass of the milky way galaxy. It may be demonstrated that the primitive chemistry of the earth's surface was dominated by these extraterrestrial molecules after aggregated into comets if the rate of comet impacts with the earth was comparable with that required to account for the extinction of species over the past 300 million years. Ultraviolet irradiation of bacterial spores has been studied for the first time under simulated interstellar conditions. The inactivation time predicted for the less dense regions of space is at most several hundred years. Within molecular clouds it is shown on theoretical and experimental grounds that this time may be extended to tens of million of years which is the estimated time required for their transport from one solar system to another by a molecular cloud. However survival of spores during their initial exposure to the solar ultraviolet presents a problem for panspermia because it requires that in the process of ejection from the earth's surface they must be enclosed within a cocoon (or mantle) of ultraviolet absorbing material of approximately 0.6 micrometer thickness. Thus, although panspermia can not be rejected on the basis of lack of interstellar survival there may remain insurmountable obstacles to its occurring because of the very special protective shield requirements during ejection from its planetary source.

Bacillus subtilis↗

PubMed2005

Collagen orientation patterns in human secondary osteons, quantified in the radial direction by confocal microscopy.

The composite structure of secondary osteon lamellae, key micro-mechanical components of human bone, has intrigued researchers for the last 300 years. Scanning confocal microscopy here for the first time systematically quantifies collagen orientations by location within the lamellar thickness. Fully calcified lamellar specimens, extinct or bright in cross-section under circularly polarized light, were gently flattened, and then examined along their thickness direction, the radial direction in the previously embedding osteon. Collagen orientation was measured from confocal image stacks. So-called extinct lamellae and so-called bright lamellae are found to display distinct, characteristic patterns of collagen orientation distribution. Orientations longitudinal to the osteon axis in extinct lamellae, transverse to the osteon axis in bright lamellae, and oblique to the osteon axis in both lamellar types, show parabolic distribution through specimen thickness. Longitudinal collagen in extinct lamellae, and transverse collagen in bright lamellae, peaks at middle third of lamellar thickness, while oblique collagen peaks at outer thirds of both types. Throughout the thickness, longitudinal collagen orientations characterize extinct lamellar specimens, while orientations oblique to the original osteon axis characterize bright lamellar specimens. Measured patterns complement previous indirect results by different methods and reinforce previously hypothesized differences in lamellar mechanical functions.

Adult↗

PubMed2004

Spatial heterogeneity and the persistence of infectious diseases.

The endemic persistence of infectious diseases can often not be understood without taking into account the relevant heterogeneities of host mixing. Here, we consider spatial heterogeneity, defined as 'patchiness' of the host population. After briefly reviewing how disease persistence is influenced by population size, reproduction number and infectious period, we explore its dependence on the level of spatial heterogeneity. Analysis and simulation of disease transmission in a symmetric meta-population suggest that disease persistence typically becomes worse as spatial heterogeneity increases, although local persistence optima can occur for infections with oscillatory population dynamics. We obtain insight into the dynamics that underlie the observed persistence patterns by studying the infection prevalence correlation between patches and by comparing full-model simulations to results obtained using simplified patch-level descriptions of the interplay between local extinctions and between-patch transmissions. The observed patterns are interpreted in terms of rescue effects for strong spatial heterogeneity and in terms of between-patch coherence and synchronization effects at intermediate and weak levels of heterogeneity.

Communicable Diseases↗

PubMed2006

A multi-compartment cell repopulation model allowing for inter-compartmental migration following radiation exposure, applied to leukaemia.

There is much uncertainty about cancer risks at the high radiation doses used in radiotherapy (RT). It has generally been assumed that cancer induction decreases rapidly at high doses due to cell killing. However, this is not seen in all RT groups, and a model recently developed by Sachs and Brenner [2005. Solid tumor risks after high doses of ionizing radiation. Proc. Natl Acad. Sci. USA 102, 13040-13045] proposed a mechanism for repopulation of cells after radiation exposure that explained why this might happen, at least for solid tumours. In this paper, this model is generalized to allow for heterogeneity in the dose received, and various alternate patterns of repopulation are also considered. The model is fitted to the Japanese atomic bomb survivor leukaemia incidence data, and data for various therapeutically irradiated groups. Two sets of parameters from these model fits are used to assess the sensitivity of model predictions. It is shown that in general allowing for heterogeneity in dose distribution and haematopoietic stem cell migration results in lower risks than the same average dose administered uniformly and without such migration, although this does not hold in the limiting case of complete stem cell repopulation between radiation dose fractions. We also investigate the difference made by assuming a compartmental repopulation signal, and a global repopulation signal. In general we show that in the absence of stochastic extinction, compartmental repopulation always predicts a larger number of mutated cells than global repopulation. However, in certain dose regimes stochastic extinction cannot be ignored, and in these cases the numbers of mutated cells predicted with global repopulation can exceed that for compartmental repopulation. In general, mutant cell numbers are highly overdispersed, with variance much greater than the mean.

Cell Count↗

PubMed2006

Spatially extended host-parasite interactions: the role of recovery and immunity.

Techniques for determining the long-term dynamics of host-parasite systems are well established for mixed populations. The field of spatial modelling in ecology is more recent but a number of key advances have been made. In this paper, we use state-of-the-art approximation techniques, supported by simulations, in order to investigate the role of recovery and immunity in spatially structured populations. Our approach is to use correlation models, namely pair-wise models, to capture the spatial relationships of contacts and interactions between individuals. We use the pair-wise framework to address a number of key ecological questions; including, the persistence of endemic limit cycles and regions of parasite-driven extinction--features which differentiate spatial from non-spatial models--and the effects on invasion fitness. We demonstrate a loss of limit cycle behaviour, in addition to an increase in the critical transmissibility and extinction thresholds, when recovery is included. This approach allows for a better analytical understanding of the dynamics of host-parasite interactions and demonstrates the importance of recovery and immunity in local interactions.

Animals↗

PubMed2001

Chromosome races with Pliocene origins: evidence from mtDNA.

There are eight distinct chromosomal races of the New Zealand weta Hemideina thoracica. We used mtDNA sequence data to test the hypothesis that these races originated on islands during the early Pliocene (7--4 million years ago). Nine major mitochondrial lineages were identified from 65 cytochrome oxidase I sequences. Phylogenetic analysis of these lineages suggests that they arose at approximately the same time. The geographical distribution of some lineages coincides with areas that were islands during the Pliocene. Overall, hierarchical AMOVA analysis shows that chromosomal races and Pliocene islands describe only 28% and 24%, respectively, of the total current mtDNA variation. However, removing one widespread (A) and one putatively introgressed (F) lineage increases these estimates to 65% and 80%, respectively. Intraspecific sequence divergence was very high, reaching a maximum of 9.5% (uncorrected distance) and GC content was high compared to other insect mtDNA sequences. Average corrected distance among mtDNA lineages supports the Pliocene origins of this level of genetic diversity. In the southern part of the species range there is reduced mtDNA variation, probably related to local extinction of H. thoracica populations from recent volcanic activity and subsequent re-colonization from a leading edge. In contrast, in this southern part there are five chromosome races, suggesting that chromosome races here may be younger than those in the north.

Animals↗

PubMed1972

Nonmathematical models for evolution of altruism, and for group selection (peck order-territoriality-ant colony-dual-determinant model-tri-determinant model).

Mathematical biologists have failed to produce a satisfactory general model for evolution of altruism, i.e., of behaviors by which "altruists" benefit other individuals but not themselves; kin selection does not seem to be a sufficient explanation of nonreciprocal altruism. Nonmathematical (but mathematically acceptable) models are now proposed for evolution of negative altruism in dual-determinant and of positive altruism in tri-determinant systems. Peck orders, territorial systems, and an ant society are analyzed as examples. In all models, evolution is primarily by individual selection, probably supplemented by group selection. Group selection is differential extinction of populations. It can act only on populations preformed by selection at the individual level, but can either cancel individual selective trends (effecting evolutionary homeostasis) or supplement them; its supplementary effect is probably increasingly important in the evolution of increasingly organized populations.

Animals↗

PubMed2002

A review of the population biology and host-parasite interactions of the sea louse Lepeophtheirus salmonis (Copepoda: Caligidae).

Lepeophtheirus salmonis is a specific parasite of salmonids that occurs in the Atlantic and Pacific Oceans. When infestations are heavy fish mortality can occur although the factors that are responsible for causing epizootics, especially in wild salmonid populations are still largely unknown. Over the past 20 years this parasite has caused significant economic losses in farmed salmon production and possibly in wild salmonid populations locally. Understanding the connectivity between populations is crucial to an understanding of the epidemiology of infections and for management of infections in aquaculture. Data from genetics, pesticide resistance, larval dispersal models and spatial and temporal patterns of infestation in wild and farmed hosts suggests a spatially highly structured metapopulation the components of which have different levels of connectivity, probabilities of extinction and influence on the development of local infestations. The population structure is defined mainly by the dispersal dynamics of the planktonic stages and the behaviour of the host. Until recently virtually nothing was known about the relationship between the parasite and the host, or how the host may influence lice at local or population level. Typically, impacts on the host have usually been reported in terms of pathological lesions caused by attachment and feeding of the adult stages, as well as localised mild epithelial responses to juvenile attachment. However many studies report pathology associated with severe infestation. Recent new studies on the host-parasite interactions of L. salmonis have shown that this parasite induces stress-related responses systemically in the host skin and gills and that the stress response and immune systems are modulated. In the second part of this review, these new studies are presented, together with results from other host-parasite model systems where data for caligid sea lice are missing. One of the most revealing methods reported recently is the application of a net confinement stressor to examine modulation of the stress response and immune system of the host fish. This approach has shown that although until now, infective stages of L. salmonis were not thought to affect the host, they do induce systematic effects in the host that result in a stress response and modulated immune system. Host-parasite interactions affecting these stress responses and the immune system may be key factors in facilitating epizootics by reducing the host's ability to reject the parasites, as well as reducing disease resistance under some environmental conditions. The host-parasite interaction therefore needs to be incorporated into any model of population structure and dynamics.

Animals↗

PubMed1998

Ecological mechanisms of evolution by natural selection: causal processes generating density-and-frequency dependent fitness.

The current theory of natural selection explains that adaptive evolution occurs because genotypes with greater survival or reproductive tendencies, due to their particular biological properties, tend to increase in frequency over the lesser ones in a common environment; therefore, the former will eventually replace the latter. In nature, such a selection process most often occurs in a local population which is nested in a community involving local ecological dynamics which are not clearly articulated in the explanatory scheme of the theory. This paper seeks to explicate such an ecological process giving rise to the evolution of a local population with a particular focus on dynamic effects of an increase in the number of invasive, new types on the fate of old ones. Arguments using the ecological-mechanistic model, representing negative interactions among alternative types of organisms, suggest major ecological mechanisms by which the new replace the old; a selective increase in the number of one type leads to a decrease in the equilibrial abundance of a limiting resource, an increase in the density of conspecifics, and/or an increase in the density of predators, which would in turn lower the per capita reproductive rate, or raise the morality rate of another and make it extinct. Thus, replacement due to selection is associated with such dynamic shifts in equilibria occurring in a local community. The analysis of three (a resource, a prey and a predator) and four species (those plus a top predator) models suggests that evolutionary processes cannot be predicted without reference to the web structure of the community, that some fitness components causing a selective increase in a particular type can have, in some cases, nothing to do with factors causing selective decreases in alternatives, and that evolution of some traits can occur without resource competition.

Animals↗