Active-to-absorbing-state phase transition in an evolving population with mutation.

PubMed

Sarkar, Niladri

2015-10-01

We study the active to absorbing phase transition (AAPT) in a simple two-component model system for a species and its mutant. We uncover the nontrivial critical scaling behavior and weak dynamic scaling near the AAPT that shows the significance of mutation and highlights the connection of this model with the well-known directed percolation universality class. Our model should be a useful starting point to study how mutation may affect extinction or survival of a species.

Finding evolved stars in the inner Galactic disk with Gaia

NASA Astrophysics Data System (ADS)

Quiroga-Nuñez, L. H.; van Langevelde, H. J.; Pihlström, Y. M.; Sjouwerman, L. O.; Brown, A. G. A.

2018-04-01

The Bulge Asymmetries and Dynamical Evolution (BAaDE) survey will provide positions and line-of-sight velocities of ~20, 000 evolved, maser bearing stars in the Galactic plane. Although this Galactic region is affected by optical extinction, BAaDE targets may have Gaia cross-matches, eventually providing additional stellar information. In an initial attempt to cross-match BAaDE targets with Gaia, we have found more than 5,000 candidates. Of these, we may expect half to show SiO emission, which will allow us to obtain velocity information. The cross-match is being refined to avoid false positives using different criteria based on distance analysis, flux variability, and color assessment in the mid- and near-IR. Once the cross-matches can be confirmed, we will have a unique sample to characterize the stellar population of evolved stars in the Galactic bulge, which can be considered fossils of the Milky Way formation.

A crucial step toward realism: responses to climate change from an evolving metacommunity perspective.

PubMed

Urban, Mark C; De Meester, Luc; Vellend, Mark; Stoks, Robby; Vanoverbeke, Joost

2012-02-01

We need to understand joint ecological and evolutionary responses to climate change to predict future threats to biological diversity. The 'evolving metacommunity' framework emphasizes that interactions between ecological and evolutionary mechanisms at both local and regional scales will drive community dynamics during climate change. Theory suggests that ecological and evolutionary dynamics often interact to produce outcomes different from those predicted based on either mechanism alone. We highlight two of these dynamics: (i) species interactions prevent adaptation of nonresident species to new niches and (ii) resident species adapt to changing climates and thereby prevent colonization by nonresident species. The rate of environmental change, level of genetic variation, source-sink structure, and dispersal rates mediate between these potential outcomes. Future models should evaluate multiple species, species interactions other than competition, and multiple traits. Future experiments should manipulate factors such as genetic variation and dispersal to determine their joint effects on responses to climate change. Currently, we know much more about how climates will change across the globe than about how species will respond to these changes despite the profound effects these changes will have on global biological diversity. Integrating evolving metacommunity perspectives into climate change biology should produce more accurate predictions about future changes to species distributions and extinction threats.

A crucial step toward realism: responses to climate change from an evolving metacommunity perspective

PubMed Central

Urban, Mark C; De Meester, Luc; Vellend, Mark; Stoks, Robby; Vanoverbeke, Joost

2012-01-01

We need to understand joint ecological and evolutionary responses to climate change to predict future threats to biological diversity. The ‘evolving metacommunity’ framework emphasizes that interactions between ecological and evolutionary mechanisms at both local and regional scales will drive community dynamics during climate change. Theory suggests that ecological and evolutionary dynamics often interact to produce outcomes different from those predicted based on either mechanism alone. We highlight two of these dynamics: (i) species interactions prevent adaptation of nonresident species to new niches and (ii) resident species adapt to changing climates and thereby prevent colonization by nonresident species. The rate of environmental change, level of genetic variation, source-sink structure, and dispersal rates mediate between these potential outcomes. Future models should evaluate multiple species, species interactions other than competition, and multiple traits. Future experiments should manipulate factors such as genetic variation and dispersal to determine their joint effects on responses to climate change. Currently, we know much more about how climates will change across the globe than about how species will respond to these changes despite the profound effects these changes will have on global biological diversity. Integrating evolving metacommunity perspectives into climate change biology should produce more accurate predictions about future changes to species distributions and extinction threats. PMID:25568038

Basins of coexistence and extinction in spatially extended ecosystems of cyclically competing species.

PubMed

Ni, Xuan; Yang, Rui; Wang, Wen-Xu; Lai, Ying-Cheng; Grebogi, Celso

2010-12-01

Microscopic models based on evolutionary games on spatially extended scales have recently been developed to address the fundamental issue of species coexistence. In this pursuit almost all existing works focus on the relevant dynamical behaviors originated from a single but physically reasonable initial condition. To gain comprehensive and global insights into the dynamics of coexistence, here we explore the basins of coexistence and extinction and investigate how they evolve as a basic parameter of the system is varied. Our model is cyclic competitions among three species as described by the classical rock-paper-scissors game, and we consider both discrete lattice and continuous space, incorporating species mobility and intraspecific competitions. Our results reveal that, for all cases considered, a basin of coexistence always emerges and persists in a substantial part of the parameter space, indicating that coexistence is a robust phenomenon. Factors such as intraspecific competition can, in fact, promote coexistence by facilitating the emergence of the coexistence basin. In addition, we find that the extinction basins can exhibit quite complex structures in terms of the convergence time toward the final state for different initial conditions. We have also developed models based on partial differential equations, which yield basin structures that are in good agreement with those from microscopic stochastic simulations. To understand the origin and emergence of the observed complicated basin structures is challenging at the present due to the extremely high dimensional nature of the underlying dynamical system. © 2010 American Institute of Physics.

Can oncology recapitulate paleontology? Lessons from species extinctions

PubMed Central

Walther, Viola; Hiley, Crispin T.; Shibata, Darryl; Swanton, Charles; Turner, Paul E.; Maley, Carlo C.

2015-01-01

Although we can treat cancers with cytotoxic chemotherapies, target them with molecules that bind to oncogenic drivers, and induce substantial cell death with radiation, local and metastatic tumours recur, resulting in extensive morbidity and mortality. It is difficult to drive a tumour to extinction. Geographically dispersed species are perhaps equally resistant to extinction, but >99.9% of species that have ever existed have become extinct. By contrast, we are nowhere near that level of success in cancer therapy. The phenomena are broadly analogous. In both cases, a genetically diverse population mutates and evolves through natural selection. The goal of cancer therapy is to cause cancer cell population extinction or at least to limit any further increase in population size, so the tumour burden does not overwhelm the patient. However, despite available treatments, complete responses are rare, and partial responses are limited in duration. Many patients eventually relapse with tumours that evolve from cells that survive therapy. Similarly, species are remarkably resilient to environmental change. Paleontology can show us the conditions that lead to extinction and the characteristics of species that make them resistant to extinction. These lessons could be translated to improve cancer therapy and prognosis. PMID:25687908

Chemistry in dynamically evolving clouds

NASA Technical Reports Server (NTRS)

Tarafdar, S. P.; Prasad, S. S.; Huntress, W. T., Jr.; Villere, K. R.; Black, D. C.

1985-01-01

A unified model of chemical and dynamical evolution of isolated, initially diffuse and quiescent interstellar clouds is presented. The model uses a semiempirically derived dependence of the observed cloud temperatures on the visual extinction and density. Even low-mass, low-density, diffuse clouds can collapse in this model, because the inward pressure gradient force assists gravitational contraction. In contrast, previous isothermal collapse models required the low-mass diffuse clouds to be unrealistically cold before gravitational contraction could start. Theoretically predicted dependences of the column densities of various atoms and molecules, such as C and CO, on visual extinction in diffuse clouds are in accord with observations. Similarly, the predicted dependences of the fractional abundances of various chemical species (e.g., CO, H2CO, HCN, HCO(+)) on the total hydrogen density in the core of the dense clouds also agree with observations reported to date in the literature. Compared with previous models of interstellar chemistry, the present model has the potential to explain the wide spectrum of chemical and physical properties of both diffuse and dense clouds with a common formalism employing only a few simple initial conditions.

Altruistic aging: The evolutionary dynamics balancing longevity and evolvability.

PubMed

Herrera, Minette; Miller, Aaron; Nishimura, Joel

2017-04-01

Altruism is typically associated with traits or behaviors that benefit the population as a whole, but are costly to the individual. We propose that, when the environment is rapidly changing, senescence (age-related deterioration) can be altruistic. According to numerical simulations of an agent-based model, while long-lived individuals can outcompete their short lived peers, populations composed of long-lived individuals are more likely to go extinct during periods of rapid environmental change. Moreover, as in many situations where other cooperative behavior arises, senescence can be stabilized in a structured population.

Rapid evolution of mimicry following local model extinction.

PubMed

Akcali, Christopher K; Pfennig, David W

2014-06-01

Batesian mimicry evolves when individuals of a palatable species gain the selective advantage of reduced predation because they resemble a toxic species that predators avoid. Here, we evaluated whether-and in which direction-Batesian mimicry has evolved in a natural population of mimics following extirpation of their model. We specifically asked whether the precision of coral snake mimicry has evolved among kingsnakes from a region where coral snakes recently (1960) went locally extinct. We found that these kingsnakes have evolved more precise mimicry; by contrast, no such change occurred in a sympatric non-mimetic species or in conspecifics from a region where coral snakes remain abundant. Presumably, more precise mimicry has continued to evolve after model extirpation, because relatively few predator generations have passed, and the fitness costs incurred by predators that mistook a deadly coral snake for a kingsnake were historically much greater than those incurred by predators that mistook a kingsnake for a coral snake. Indeed, these results are consistent with prior theoretical and empirical studies, which revealed that only the most precise mimics are favoured as their model becomes increasingly rare. Thus, highly noxious models can generate an 'evolutionary momentum' that drives the further evolution of more precise mimicry-even after models go extinct. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Rapid evolution of mimicry following local model extinction

PubMed Central

Akcali, Christopher K.; Pfennig, David W.

2014-01-01

Batesian mimicry evolves when individuals of a palatable species gain the selective advantage of reduced predation because they resemble a toxic species that predators avoid. Here, we evaluated whether—and in which direction—Batesian mimicry has evolved in a natural population of mimics following extirpation of their model. We specifically asked whether the precision of coral snake mimicry has evolved among kingsnakes from a region where coral snakes recently (1960) went locally extinct. We found that these kingsnakes have evolved more precise mimicry; by contrast, no such change occurred in a sympatric non-mimetic species or in conspecifics from a region where coral snakes remain abundant. Presumably, more precise mimicry has continued to evolve after model extirpation, because relatively few predator generations have passed, and the fitness costs incurred by predators that mistook a deadly coral snake for a kingsnake were historically much greater than those incurred by predators that mistook a kingsnake for a coral snake. Indeed, these results are consistent with prior theoretical and empirical studies, which revealed that only the most precise mimics are favoured as their model becomes increasingly rare. Thus, highly noxious models can generate an ‘evolutionary momentum’ that drives the further evolution of more precise mimicry—even after models go extinct. PMID:24919704

Network Analysis of Earth's Co-Evolving Geosphere and Biosphere

NASA Astrophysics Data System (ADS)

Hazen, R. M.; Eleish, A.; Liu, C.; Morrison, S. M.; Meyer, M.; Consortium, K. D.

2017-12-01

A fundamental goal of Earth science is the deep understanding of Earth's dynamic, co-evolving geosphere and biosphere through deep time. Network analysis of geo- and bio- `big data' provides an interactive, quantitative, and predictive visualization framework to explore complex and otherwise hidden high-dimension features of diversity, distribution, and change in the evolution of Earth's geochemistry, mineralogy, paleobiology, and biochemistry [1]. Networks also facilitate quantitative comparison of different geological time periods, tectonic settings, and geographical regions, as well as different planets and moons, through network metrics, including density, centralization, diameter, and transitivity.We render networks by employing data related to geographical, paragenetic, environmental, or structural relationships among minerals, fossils, proteins, and microbial taxa. An important recent finding is that the topography of many networks reflects parameters not explicitly incorporated in constructing the network. For example, networks for minerals, fossils, and protein structures reveal embedded qualitative time axes, with additional network geometries possibly related to extinction and/or other punctuation events (see Figure). Other axes related to chemical activities and volatile fugacities, as well as pressure and/or depth of formation, may also emerge from network analysis. These patterns provide new insights into the way planets evolve, especially Earth's co-evolving geosphere and biosphere. 1. Morrison, S.M. et al. (2017) Network analysis of mineralogical systems. American Mineralogist 102, in press. Figure Caption: A network of Phanerozoic Era fossil animals from the past 540 million years includes blue, red, and black circles (nodes) representing family-level taxa and grey lines (links) between coexisting families. Age information was not used in the construction of this network; nevertheless an intrinsic timeline is embedded in the network topology. In addition, two mass extinction events appear as "pinch points" in the network.

Multi-photon UV photolysis of gaseous polycyclic aromatic hydrocarbons: Extinction spectra and dynamics

NASA Astrophysics Data System (ADS)

Walsh, A. J.; Ruth, A. A.; Gash, E. W.; Mansfield, M. W. D.

2013-08-01

The extinction spectra of static naphthalene and static biphenylene vapor, each buffered with a noble gas at room temperature, were measured as a function of time in the region between 390 and 850 nm after UV multi-photon laser photolysis at 308 nm. Employing incoherent broadband cavity enhanced absorption spectroscopy (IBBCEAS), the spectra were found to be unstructured with a general lack of isolated features suggesting that the extinction was not solely based on absorption but was in fact dominated by scattering from particles formed in the photolysis of the respective polycyclic aromatic hydrocarbon. Following UV multi-photon photolysis, the extinction dynamics of the static (unstirred) closed gas-phase system exhibits extraordinary quasi-periodic and complex oscillations with periods ranging from seconds to many minutes, persisting for up to several hours. Depending on buffer gas type and pressure, several types of dynamical responses could be generated (classified as types I, II, and III). They were studied as a function of temperature and chamber volume for different experimental conditions and possible explanations for the oscillations are discussed. A conclusive model for the observed phenomena has not been established. However, a number of key hypotheses have made based on the measurements in this publication: (a) Following the multi-photon UV photolysis of naphthalene (or biphenylene), particles are formed on a timescale not observable using IBBCEAS. (b) The observed temporal behavior cannot be described on basis of a chemical reaction scheme alone. (c) The pressure dependence of the system's responses is due to transport phenomena of particles in the chamber. (d) The size distribution and the refractive indices of particles are time dependent and evolve on a timescale of minutes to hours. The rate of particle coagulation, involving coalescent growth and particle agglomeration, affects the observed oscillations. (e) The walls of the chamber act as a sink. The wall conditions (which could not be quantitatively characterized) have a profound influence on the dynamics of the system and on its slow return to an equilibrium state.

What Do We Know About the Ultraviolet Extinction Curve, Fifty Years After the Discovery of the Bump?

NASA Astrophysics Data System (ADS)

Clayton, Geoffrey C.

2012-05-01

It is almost 50 years since Ted Stecher reported the discovery of the 2175 A bump, and almost 25 years since CCM characterized the UV extinction curve as a one-parameter function of R(V), the ratio of total-to-selective extinction. Great strides have been made since then in laboratory, theory, and observation but many questions still remain. The bump is still an unidentified feature, and CCM is not a reliable guide to the wavelength dependence of dust extinction beyond the Milky Way. In fact, the average extinction curve of SMC dust, which has little or no evidence for a 2175 A bump, may be more common in extragalactic environments than Milky Way type dust. The UV extinction curve has been extended to the Lyman limit without any sign in a turnover in the far-UV rise. The old standbys, silicates, graphite, amorphous carbon, and PAH's are still the go-to grain types. But many questions remain about how global properties such as metallicity may lead to large variations in the extinction properties from one galaxy to another. Also of great interest is how dust grains are created, evolve and are destroyed, and in particular, what fraction comes from sources such as evolved stars and supernovae, and what fraction is grown in the ISM. I plan to summarize the role of laboratory and theory can play in better understanding the interstellar dust grains responsible UV extinction.

Long-Distance Rescue and Slow Extinction Dynamics Govern Multiscale Metapopulations.

PubMed

Huth, Géraldine; Haegeman, Bart; Pitard, Estelle; Munoz, François

2015-10-01

Rare long-distance dispersal is known to be critical for species dynamics, but how the interplay between short- and long-distance colonization influences regional persistence in a fragmented habitat remains poorly understood. We propose a metapopulation model that combines local colonization within habitat islands and long-distance colonization between islands. We study how regional occupancy dynamics are affected by the multiscale colonization process. We find that the island size distribution (ISD) is a key driver of the long-term occupancy dynamics. When the ISD is heterogeneous-that is, when the size of islands is variable-we show that extinction dynamics become very slow. We demonstrate that this behavior is unrelated to the well-known extinction debt near the critical extinction threshold. Hence, this finding questions the equivalence between extinction debt and critical transitions in the context of metapopulation collapse. Furthermore, we show that long-distance colonization can rescue small islands from extinction and sustain a steady regional occupancy. These results provide novel theoretical and practical insights into extinction dynamics and persistence in fragmented habitats and are thus relevant for the design of conservation strategies.

Life in the Aftermath of Mass Extinctions.

PubMed

Hull, Pincelli

2015-10-05

The vast majority of species that have ever lived went extinct sometime other than during one of the great mass extinction events. In spite of this, mass extinctions are thought to have outsized effects on the evolutionary history of life. While part of this effect is certainly due to the extinction itself, I here consider how the aftermaths of mass extinctions might contribute to the evolutionary importance of such events. Following the mass loss of taxa from the fossil record are prolonged intervals of ecological upheaval that create a selective regime unique to those times. The pacing and duration of ecosystem change during extinction aftermaths suggests strong ties between the biosphere and geosphere, and a previously undescribed macroevolutionary driver - earth system succession. Earth system succession occurs when global environmental or biotic change, as occurs across extinction boundaries, pushes the biosphere and geosphere out of equilibrium. As species and ecosystems re-evolve in the aftermath, they change global biogeochemical cycles - and in turn, species and ecosystems - over timescales typical of the geosphere, often many thousands to millions of years. Earth system succession provides a general explanation for the pattern and timing of ecological and evolutionary change in the fossil record. Importantly, it also suggests that a speed limit might exist for the pace of global biotic change after massive disturbance - a limit set by geosphere-biosphere interactions. For mass extinctions, earth system succession may drive the ever-changing ecological stage on which species evolve, restructuring ecosystems and setting long-term evolutionary trajectories as they do. Copyright © 2015 Elsevier Ltd. All rights reserved.

Extinction and the spatial dynamics of biodiversity

PubMed Central

Jablonski, David

2008-01-01

The fossil record amply shows that the spatial fabric of extinction has profoundly shaped the biosphere; this spatial dimension provides a powerful context for integration of paleontological and neontological approaches. Mass extinctions evidently alter extinction selectivity, with many factors losing effectiveness except for a positive relation between survivorship and geographic range at the clade level (confirmed in reanalyses of end-Cretaceous extinction data). This relation probably also holds during “normal” times, but changes both slope and intercept with increasing extinction. The strong geographical component to clade dynamics can obscure causation in the extinction of a feature or a clade, owing to hitchhiking effects on geographic range, so that multifactorial analyses are needed. Some extinctions are spatially complex, and regional extinctions might either reset a diversity ceiling or create a diversification debt open to further diversification or invasion. Evolutionary recoveries also exhibit spatial dynamics, including regional differences in invasibilty, and expansion of clades from the tropics fuels at least some recoveries, as well as biodiversity dynamics during normal times. Incumbency effects apparently correlate more closely with extinction intensities than with standing diversities, so that regions with higher local and global extinctions are more subject to invasion; the latest Cenozoic temperate zones evidently received more invaders than the tropics or poles, but this dynamic could shift dramatically if tropical diversity is strongly depleted. The fossil record can provide valuable insights, and their application to present-day issues will be enhanced by partitioning past and present-day extinctions by driving mechanism rather than emphasizing intensity. PMID:18695229

Species Turnover through Time: Colonization and Extinction Dynamics across Metacommunities.

PubMed

Nuvoloni, Felipe Micali; Feres, Reinaldo José Fazzio; Gilbert, Benjamin

2016-06-01

Island biogeography and metacommunity theory often use equilibrium assumptions to predict local diversity, yet nonequilibrium dynamics are common in nature. In nonequilibrium communities, local diversity fluctuates through time as the relative importance of colonization and extinction change. Here, we test the prevalence and causes of nonequilibrium dynamics in metacommunities of mites associated with rubber trees distributed over large spatial (>1,000 km) and temporal (>30-60 generations) scales in Brazil. We measured colonization and extinction rates to test species turnover and nonequilibrium dynamics over a growing season. Mite metacommunities exhibited nonequilibrium dynamics for most months of the year, and these dynamics tracked climatic conditions. Monthly shifts in temperature of more than 1°C resulted in nonequilibrium dynamics, as did mean temperatures outside of two critical ranges. Nonequilibrium dynamics were caused by a change in colonization with temperature change and changes in both colonization and extinction with absolute temperature. Species turnover showed different trends; high relative humidity increased both colonization and extinction rates, increasing turnover but not nonequilibrium dynamics. Our study illustrates that testing nonequilibrium dynamics can provide new insights into the drivers of colonization, extinction, and diversity fluctuations in metacommunities.

Community stability and selective extinction during the Permian-Triassic mass extinction

NASA Astrophysics Data System (ADS)

Roopnarine, Peter D.; Angielczyk, Kenneth D.

2015-10-01

The fossil record contains exemplars of extreme biodiversity crises. Here, we examined the stability of terrestrial paleocommunities from South Africa during Earth's most severe mass extinction, the Permian-Triassic. We show that stability depended critically on functional diversity and patterns of guild interaction, regardless of species richness. Paleocommunities exhibited less transient instability—relative to model communities with alternative community organization—and significantly greater probabilities of being locally stable during the mass extinction. Functional patterns that have evolved during an ecosystem's history support significantly more stable communities than hypothetical alternatives.

Symmetry of interactions rules in incompletely connected random replicator ecosystems.

PubMed

Kärenlampi, Petri P

2014-06-01

The evolution of an incompletely connected system of species with speciation and extinction is investigated in terms of random replicators. It is found that evolving random replicator systems with speciation do become large and complex, depending on speciation parameters. Antisymmetric interactions result in large systems, whereas systems with symmetric interactions remain small. A co-dominating feature is within-species interaction pressure: large within-species interaction increases species diversity. Average fitness evolves in all systems, however symmetry and connectivity evolve in small systems only. Newcomers get extinct almost immediately in symmetric systems. The distribution in species lifetimes is determined for antisymmetric systems. The replicator systems investigated do not show any sign of self-organized criticality. The generalized Lotka-Volterra system is shown to be a tedious way of implementing the replicator system.

Multi-photon UV photolysis of gaseous polycyclic aromatic hydrocarbons: Extinction spectra and dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walsh, A. J.; Gash, E. W.; Mansfield, M. W. D.

The extinction spectra of static naphthalene and static biphenylene vapor, each buffered with a noble gas at room temperature, were measured as a function of time in the region between 390 and 850 nm after UV multi-photon laser photolysis at 308 nm. Employing incoherent broadband cavity enhanced absorption spectroscopy (IBBCEAS), the spectra were found to be unstructured with a general lack of isolated features suggesting that the extinction was not solely based on absorption but was in fact dominated by scattering from particles formed in the photolysis of the respective polycyclic aromatic hydrocarbon. Following UV multi-photon photolysis, the extinction dynamicsmore » of the static (unstirred) closed gas-phase system exhibits extraordinary quasi-periodic and complex oscillations with periods ranging from seconds to many minutes, persisting for up to several hours. Depending on buffer gas type and pressure, several types of dynamical responses could be generated (classified as types I, II, and III). They were studied as a function of temperature and chamber volume for different experimental conditions and possible explanations for the oscillations are discussed. A conclusive model for the observed phenomena has not been established. However, a number of key hypotheses have made based on the measurements in this publication: (a) Following the multi-photon UV photolysis of naphthalene (or biphenylene), particles are formed on a timescale not observable using IBBCEAS. (b) The observed temporal behavior cannot be described on basis of a chemical reaction scheme alone. (c) The pressure dependence of the system's responses is due to transport phenomena of particles in the chamber. (d) The size distribution and the refractive indices of particles are time dependent and evolve on a timescale of minutes to hours. The rate of particle coagulation, involving coalescent growth and particle agglomeration, affects the observed oscillations. (e) The walls of the chamber act as a sink. The wall conditions (which could not be quantitatively characterized) have a profound influence on the dynamics of the system and on its slow return to an equilibrium state.« less

The division of labor: genotypic versus phenotypic specialization.

PubMed

Wahl, L M

2002-07-01

A model of the division of labor in simple evolving systems is explored to compare two strategies evident in natural populations: phenotypic specialization (such as differentiation by regulated gene expression) and genotypic specialization (such as co-infection by complementary covirus populations). While genotypic specialization is vulnerable to the chance extinction of an essential specialist type and to parasitism, phenotypic specialization is able to overcome these hurdles. When simple spatial effects are included, phenotypic specialization has further benefits, protecting against destructive dynamic patterns. Many of the advantages of phenotypic specialization, however, can only be realized when a high degree of relatedness within groups is ensured.

Direct measurements of the optical cross sections and refractive indices of individual volatile and hygroscopic aerosol particles.

PubMed

Mason, B J; Cotterell, M I; Preston, T C; Orr-Ewing, A J; Reid, J P

2015-06-04

We present measurements of the evolving extinction cross sections of individual aerosol particles (spanning 700-2500 nm in radius) during the evaporation of volatile components or hygroscopic growth using a combination of a single particle trap formed from a Bessel light beam and cavity ring-down spectroscopy. For single component organic aerosol droplets of 1,2,6-hexanetriol, polyethylene glycol 400, and glycerol, the slow evaporation of the organic component (over time scales of 1000 to 10,000 s) leads to a time-varying size and extinction cross section that can be used to estimate the refractive index of the droplet. Measurements on binary aqueous-inorganic aerosol droplets containing one of the inorganic solutes ammonium bisulfate, ammonium sulfate, sodium nitrate, or sodium chloride (over time scales of 1000 to 15,000 s) under conditions of changing relative humidity show that extinction cross-section measurements are consistent with expectations from accepted models for the variation in droplet refractive index with hygroscopic growth. In addition, we use these systems to establish an experimental protocol for future single particle extinction measurements. The advantages of mapping out the evolving light extinction cross-section of an individual particle over extended time frames accompanied by hygroscopic cycling or component evaporation are discussed.

Unusual dynamics of extinction in a simple ecological model.

PubMed Central

Sinha, S; Parthasarathy, S

1996-01-01

Studies on natural populations and harvesting biological resources have led to the view, commonly held, that (i) populations exhibiting chaotic oscillations run a high risk of extinction; and (ii) a decrease in emigration/exploitation may reduce the risk of extinction. Here we describe a simple ecological model with emigration/depletion that shows behavior in contrast to this. This model displays unusual dynamics of extinction and survival, where populations growing beyond a critical rate can persist within a band of high depletion rates, whereas extinction occurs for lower depletion rates. Though prior to extinction at lower depletion rates the population exhibits chaotic dynamics with large amplitudes of variation and very low minima, at higher depletion rates the population persists at chaos but with reduced variation and increased minima. For still higher values, within the band of persistence, the dynamics show period reversal leading to stability. These results illustrate that chaos does not necessarily lead to population extinction. In addition, the persistence of populations at high depletion rates has important implications in the considerations of strategies for the management of biological resources. PMID:8643661

Lateral Gene Transfer from the Dead

PubMed Central

Szöllősi, Gergely J.; Tannier, Eric; Lartillot, Nicolas; Daubin, Vincent

2013-01-01

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria. [Gene tree reconciliation; lateral gene transfer; macroevolution; phylogeny.] PMID:23355531

Long-term evolution of 1991 DA: A dynamically evolved extinct Halley-type comet

NASA Technical Reports Server (NTRS)

Hahn, Gerhard; Bailey, M. E.

1992-01-01

The long-term dynamical evolution of 21 variational orbits for the intermediate-period asteroid 1991 DA was followed for up to +/-10(exp 5) years from the present. 1991 DA is close to the 2:7 resonance with Jupiter; it has avoided close encounters, within 1 AU, with this planet for at least the past 30,000 years, even at the node crossing. The future evolution typically shows no close encounters with Jupiter within at least 50,000 years. This corresponds to the mean time between node crossings with either Jupiter or Saturn. Close encounters with Saturn and Jupiter lead to a chaotic evolution for the whole ensemble, while secular perturbations cause large-amplitude swings in eccentricity and inclination (the latter covering the range 15 deg approximately less than i approximately less than 85 deg) which correlate with deep excursions of the perihelion distance to values much less than 1 AU. These variations are similar to those found in P/Machholz and a variety of other high-inclination orbits, e.g., P/Hartley-IRAS. We emphasize the connection between the orbital evolution of 1991 DA and that of Halley-type comets. If 1991 DA was once a comet, it is not surprising that it is now extinct.

An extinction/reignition dynamic method for turbulent combustion

NASA Astrophysics Data System (ADS)

Knaus, Robert; Pantano, Carlos

2011-11-01

Quasi-randomly distributed locations of high strain in turbulent combustion can cause a nonpremixed or partially premixed flame to develop local regions of extinction called ``flame holes''. The presence and extent of these holes can increase certain pollutants and reduce the amount of fuel burned. Accurately modeling the dynamics of these interacting regions can improve the accuracy of combustion simulations by effectively incorporating finite-rate chemistry effects. In the proposed method, the flame hole state is characterized by a progress variable that nominally exists on the stoichiometric surface. The evolution of this field is governed by a partial-differential equation embedded in the time-dependent two-manifold of the flame surface. This equation includes advection, propagation, and flame hole formation (flame hole healing or collapse is accounted by propagation naturally). We present a computational algorithm that solves this equation by embedding it in the usual three-dimensional space. A piece-wise parabolic WENO scheme combined with a compression algorithm are used to evolve the flame hole progress variable. A key aspect of the method is the extension of the surface data to the three-dimensional space in an efficient manner. We present results of this method applied to canonical turbulent combusting flows where the flame holes interact and describe their statistics.

Trait-based diversification shifts reflect differential extinction among fossil taxa.

PubMed

Wagner, Peter J; Estabrook, George F

2014-11-18

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

Starburst Galaxies. II. Imaging and Spectroscopy of a Radio-selected Sample

NASA Astrophysics Data System (ADS)

Smith, Denise A.; Herter, Terry; Haynes, Martha P.; Beichman, C. A.; Gautier, T. N., III

1996-06-01

We present J-, H-, and K-band images and low-resolution K-band spectra of the 20 most luminous starburst galaxies from the survey of Condon, Frayer, & Broderick. Optical rotation curves are also shown for 10 of these galaxies. Near-infrared colors, optical depths, CO indices, and dynamical masses are calculated. The near-infrared colors of the starburst nuclei are significantly redder than those observed in "normal" galaxies. Together, the Brγ and radio fluxes available for five of the galaxies imply that the starbursts are heavily obscured; an average extinction of A_V_~ 25 is derived. Strong CO absorption features indicate that late-type evolved stars are present in many of the starbursts. The average dynamical mass of the starburst region is found to be (1.0 +/- 0.4) x 10^9^ M_sun_.

Dynamic occupancy models for explicit colonization processes

USGS Publications Warehouse

Broms, Kristin M.; Hooten, Mevin B.; Johnson, Devin S.; Altwegg, Res; Conquest, Loveday

2016-01-01

The dynamic, multi-season occupancy model framework has become a popular tool for modeling open populations with occupancies that change over time through local colonizations and extinctions. However, few versions of the model relate these probabilities to the occupancies of neighboring sites or patches. We present a modeling framework that incorporates this information and is capable of describing a wide variety of spatiotemporal colonization and extinction processes. A key feature of the model is that it is based on a simple set of small-scale rules describing how the process evolves. The result is a dynamic process that can account for complicated large-scale features. In our model, a site is more likely to be colonized if more of its neighbors were previously occupied and if it provides more appealing environmental characteristics than its neighboring sites. Additionally, a site without occupied neighbors may also become colonized through the inclusion of a long-distance dispersal process. Although similar model specifications have been developed for epidemiological applications, ours formally accounts for detectability using the well-known occupancy modeling framework. After demonstrating the viability and potential of this new form of dynamic occupancy model in a simulation study, we use it to obtain inference for the ongoing Common Myna (Acridotheres tristis) invasion in South Africa. Our results suggest that the Common Myna continues to enlarge its distribution and its spread via short distance movement, rather than long-distance dispersal. Overall, this new modeling framework provides a powerful tool for managers examining the drivers of colonization including short- vs. long-distance dispersal, habitat quality, and distance from source populations.

Temporal Dynamics of Recovery from Extinction Shortly after Extinction Acquisition

ERIC Educational Resources Information Center

Archbold, Georgina E.; Dobbek, Nick; Nader, Karim

2013-01-01

Evidence suggests that extinction is new learning. Memory acquisition involves both short-term memory (STM) and long-term memory (LTM) components; however, few studies have examined early phases of extinction retention. Retention of auditory fear extinction was examined at various time points. Shortly (1-4 h) after extinction acquisition…

Experience with dynamic reinforcement rates decreases resistance to extinction.

PubMed

Craig, Andrew R; Shahan, Timothy A

2016-03-01

The ability of organisms to detect reinforcer-rate changes in choice preparations is positively related to two factors: the magnitude of the change in rate and the frequency with which rates change. Gallistel (2012) suggested similar rate-detection processes are responsible for decreases in responding during operant extinction. Although effects of magnitude of change in reinforcer rate on resistance to extinction are well known (e.g., the partial-reinforcement-extinction effect), effects of frequency of changes in rate prior to extinction are unknown. Thus, the present experiments examined whether frequency of changes in baseline reinforcer rates impacts resistance to extinction. Pigeons pecked keys for variable-interval food under conditions where reinforcer rates were stable and where they changed within and between sessions. Overall reinforcer rates between conditions were controlled. In Experiment 1, resistance to extinction was lower following exposure to dynamic reinforcement schedules than to static schedules. Experiment 2 showed that resistance to presession feeding, a disruptor that should not involve change-detection processes, was unaffected by baseline-schedule dynamics. These findings are consistent with the suggestion that change detection contributes to extinction. We discuss implications of change-detection processes for extinction of simple and discriminated operant behavior and relate these processes to the behavioral-momentum based approach to understanding extinction. © 2016 Society for the Experimental Analysis of Behavior.

Predicting evolutionary rescue via evolving plasticity in stochastic environments

PubMed Central

Baskett, Marissa L.

2016-01-01

Phenotypic plasticity and its evolution may help evolutionary rescue in a novel and stressful environment, especially if environmental novelty reveals cryptic genetic variation that enables the evolution of increased plasticity. However, the environmental stochasticity ubiquitous in natural systems may alter these predictions, because high plasticity may amplify phenotype–environment mismatches. Although previous studies have highlighted this potential detrimental effect of plasticity in stochastic environments, they have not investigated how it affects extinction risk in the context of evolutionary rescue and with evolving plasticity. We investigate this question here by integrating stochastic demography with quantitative genetic theory in a model with simultaneous change in the mean and predictability (temporal autocorrelation) of the environment. We develop an approximate prediction of long-term persistence under the new pattern of environmental fluctuations, and compare it with numerical simulations for short- and long-term extinction risk. We find that reduced predictability increases extinction risk and reduces persistence because it increases stochastic load during rescue. This understanding of how stochastic demography, phenotypic plasticity, and evolution interact when evolution acts on cryptic genetic variation revealed in a novel environment can inform expectations for invasions, extinctions, or the emergence of chemical resistance in pests. PMID:27655762

Evolutionary rescue from extinction is contingent on a lower rate of environmental change.

PubMed

Lindsey, Haley A; Gallie, Jenna; Taylor, Susan; Kerr, Benjamin

2013-02-28

The extinction rate of populations is predicted to rise under increasing rates of environmental change. If a population experiencing increasingly stressful conditions lacks appropriate phenotypic plasticity or access to more suitable habitats, then genetic change may be the only way to avoid extinction. Evolutionary rescue from extinction occurs when natural selection enriches a population for more stress-tolerant genetic variants. Some experimental studies have shown that lower rates of environmental change lead to more adapted populations or fewer extinctions. However, there has been little focus on the genetic changes that underlie evolutionary rescue. Here we demonstrate that some evolutionary trajectories are contingent on a lower rate of environmental change. We allowed hundreds of populations of Escherichia coli to evolve under variable rates of increase in concentration of the antibiotic rifampicin. We then genetically engineered all combinations of mutations from isolates evolved under lower rates of environmental change. By assessing fitness of these engineered strains across a range of drug concentrations, we show that certain genotypes are evolutionarily inaccessible under rapid environmental change. Rapidly deteriorating environments not only limit mutational opportunities by lowering population size, but they can also eliminate sets of mutations as evolutionary options. As anthropogenic activities are leading to environmental change at unprecedented rapidity, it is critical to understand how the rate of environmental change affects both demographic and genetic underpinnings of evolutionary rescue.

Temporal genetic analysis of the endangered tidewater goby: extinction-colonization dynamics or drift in isolation?

PubMed

Kinziger, Andrew P; Hellmair, Michael; McCraney, W Tyler; Jacobs, David K; Goldsmith, Greg

2015-11-01

Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction-colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction-colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction-colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction-colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within-site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20-30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction-colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction-colonization dynamics or as a stand-alone tool when field data are lacking. © 2015 John Wiley & Sons Ltd.

Ontogenetic and life history trait changes associated with convergent ecological specializations in extinct ungulate mammals

PubMed Central

Gomes Rodrigues, Helder; Billet, Guillaume

2017-01-01

Investigating life history traits in mammals is crucial to understand their survival in changing environments. However, these parameters are hard to estimate in a macroevolutionary context. Here we show that the use of dental ontogenetic parameters can provide clues to better understand the adaptive nature of phenotypic traits in extinct species such as South American notoungulates. This recently extinct order of mammals evolved in a context of important geological, climatic, and environmental variations. Interestingly, notoungulates were mostly herbivorous and acquired high-crowned teeth very early in their evolutionary history. We focused on the variations in crown height, dental eruption pattern, and associated body mass of 69 notoungulate taxa, placed in their phylogenetic and geological contexts. We showed that notoungulates evolved higher crowns several times between 45 and 20 Ma, independently of the variation in body mass. Interestingly, the independent acquisitions of ever-growing teeth were systematically accompanied by eruption of molars faster than permanent premolars. These repeated associations of dental innovations have never been documented for other mammals and raise questions on their significance and causal relationships. We suggest that these correlated changes could originate from ontogenetic adjustments favored by structural constraints, and may indicate accelerated life histories. Complementarily, these more durable and efficient dentitions could be selected to cope with important ingestions of abrasive particles in the context of intensified volcanism and increasing aridity. This study demonstrates that assessing both life history and ecological traits allows a better knowledge of the specializations of extinct mammals that evolved under strong environmental constraints. PMID:28096389

Trait-based diversification shifts reflect differential extinction among fossil taxa

PubMed Central

Wagner, Peter J.; Estabrook, George F.

2014-01-01

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models. PMID:25331898

Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection.

PubMed

Ojosnegros, Samuel; Agudo, Rubén; Sierra, Macarena; Briones, Carlos; Sierra, Saleta; González-López, Claudia; Domingo, Esteban; Cristina, Juan

2008-07-17

The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction.

Environmental change makes robust ecological networks fragile

USGS Publications Warehouse

Strona, Giovanni; Lafferty, Kevin D.

2016-01-01

Complex ecological networks appear robust to primary extinctions, possibly due to consumers’ tendency to specialize on dependable (available and persistent) resources. However, modifications to the conditions under which the network has evolved might alter resource dependability. Here, we ask whether adaptation to historical conditions can increase community robustness, and whether such robustness can protect communities from collapse when conditions change. Using artificial life simulations, we first evolved digital consumer-resource networks that we subsequently subjected to rapid environmental change. We then investigated how empirical host–parasite networks would respond to historical, random and expected extinction sequences. In both the cases, networks were far more robust to historical conditions than new ones, suggesting that new environmental challenges, as expected under global change, might collapse otherwise robust natural ecosystems.

Ultraviolet studies of O and B stars in the LMC cluster NGC 2100, the SMC cluster NGC 330 and the Galactic cluster NGC 6530

NASA Technical Reports Server (NTRS)

Boehm-Vitense, E.; Hodge, P.

1984-01-01

High-resolution and low-resolution IUE spectra of O and B stars in the LMC cluster NGC 2100, the SMC cluster NGC 330, and the young Galactic cluster NGC 6530 are investigated. Temperatures and luminosities are determined. In the LMC and SMC clusters, the most luminous stars are evolved stars on the horizontal supergiant branch, while in NGC 6530 the stars are all still on the main sequence. Extinction laws were determined. They confirm the known differences between LMC and Galactic extinctions. No mass loss was detected for the evolved B stars in the LMC and SMC clusters, while the high-luminosity stars in NGC 6530 show P Cygni profiles.

Disparity changes in 370 Ma Devonian fossils: the signature of ecological dynamics?

PubMed

Girard, Catherine; Renaud, Sabrina

2012-01-01

Early periods in Earth's history have seen a progressive increase in complexity of the ecosystems, but also dramatic crises decimating the biosphere. Such patterns are usually considered as large-scale changes among supra-specific groups, including morphological novelties, radiation, and extinctions. Nevertheless, in the same time, each species evolved by the way of micro-evolutionary processes, extended over millions of years into the evolution of lineages. How these two evolutionary scales interacted is a challenging issue because this requires bridging a gap between scales of observation and processes. The present study aims at transferring a typical macro-evolutionary approach, namely disparity analysis, to the study of fine-scale evolutionary variations in order to decipher what processes actually drove the dynamics of diversity at a micro-evolutionary level. The Late Frasnian to Late Famennian period was selected because it is punctuated by two major macro-evolutionary crises, as well as a progressive diversification of marine ecosystem. Disparity was estimated through this period on conodonts, tooth-like fossil remains of small eel-like predators that were part of the nektonic fauna. The study was focused on the emblematic genus of the period, Palmatolepis. Strikingly, both crises affected an already impoverished Palmatolepis disparity, increasing risks of random extinction. The major disparity signal rather emerged as a cycle of increase and decrease in disparity during the inter-crises period. The diversification shortly followed the first crisis and might correspond to an opportunistic occupation of empty ecological niche. The subsequent oriented shrinking in the morphospace occupation suggests that the ecological space available to Palmatolepis decreased through time, due to a combination of factors: deteriorating climate, expansion of competitors and predators. Disparity changes of Palmatolepis thus reflect changes in the structure of the ecological space itself, which was prone to evolve during this ancient period where modern ecosystems were progressively shaped.

Disparity Changes in 370 Ma Devonian Fossils: The Signature of Ecological Dynamics?

PubMed Central

Girard, Catherine; Renaud, Sabrina

2012-01-01

Early periods in Earth's history have seen a progressive increase in complexity of the ecosystems, but also dramatic crises decimating the biosphere. Such patterns are usually considered as large-scale changes among supra-specific groups, including morphological novelties, radiation, and extinctions. Nevertheless, in the same time, each species evolved by the way of micro-evolutionary processes, extended over millions of years into the evolution of lineages. How these two evolutionary scales interacted is a challenging issue because this requires bridging a gap between scales of observation and processes. The present study aims at transferring a typical macro-evolutionary approach, namely disparity analysis, to the study of fine-scale evolutionary variations in order to decipher what processes actually drove the dynamics of diversity at a micro-evolutionary level. The Late Frasnian to Late Famennian period was selected because it is punctuated by two major macro-evolutionary crises, as well as a progressive diversification of marine ecosystem. Disparity was estimated through this period on conodonts, tooth-like fossil remains of small eel-like predators that were part of the nektonic fauna. The study was focused on the emblematic genus of the period, Palmatolepis. Strikingly, both crises affected an already impoverished Palmatolepis disparity, increasing risks of random extinction. The major disparity signal rather emerged as a cycle of increase and decrease in disparity during the inter-crises period. The diversification shortly followed the first crisis and might correspond to an opportunistic occupation of empty ecological niche. The subsequent oriented shrinking in the morphospace occupation suggests that the ecological space available to Palmatolepis decreased through time, due to a combination of factors: deteriorating climate, expansion of competitors and predators. Disparity changes of Palmatolepis thus reflect changes in the structure of the ecological space itself, which was prone to evolve during this ancient period where modern ecosystems were progressively shaped. PMID:22558396

Determining Mass-Loss Rates of Evolved Stars in the Galactic Bulge from Infrared Surveys

NASA Astrophysics Data System (ADS)

Riley, Allyssa; Sargent, Benjamin A.; Srinivasan, Sundar; Meixner, Margaret; Kastner, Joel H.

2018-06-01

To investigate the relationship between mass loss from evolved stars and host galaxy metallicity, we are computing the dust mass loss budget due to red supergiant (RSG) and asymptotic giant branch (AGB) stars in the Galactic Bulge and comparing this result to that previously obtained for the Magellanic Clouds. We construct spectral energy distributions (SEDs) for our candidate RSG and AGB stars using observations from various infrared surveys, including the Galactic Legacy Infrared Mid-Plane Survey Extraordinaire (GLIMPSE). Because Robitaille et al (2008, AJ, 136, 2413) have already identified Intrinsically Red Objects from the GLIMPSE I and II surveys, we use their method as a starting point and expand the study by using the GLIMPSE 3D survey. Because AGB stars can be variable, we also match the GLIMPSE I, II, and 3D sources to other surveys, such as DEEP GLIMPSE, WISE, VVV, and DENIS, in order to characterize the variability across the spectral energy distribution (SED) of each source. This allows us to determine the source’s average SED over multiple epochs. We use extinction curves derived from Spitzer studies of extinction in the Galaxy to determine the extinction corrections for our sample. To establish mass-loss rates of evolved stars in the Bulge, we use the Grid of Red supergiant and Asymptotic giant branch ModelS (GRAMS) of dust-enshrouded evolved stars (2011, A&A, 532, A54; 2011, ApJ, 728, 93). This allows us to determine the total mass return to the Bulge from these stars. This work has been supported by NASA ADAP grant 80NSSC17K0057.

A large aberrant stem ichthyosauriform indicating early rise and demise of ichthyosauromorphs in the wake of the end-Permian extinction

PubMed Central

Jiang, Da-Yong; Motani, Ryosuke; Huang, Jian-Dong; Tintori, Andrea; Hu, Yuan-Chao; Rieppel, Olivier; Fraser, Nicholas C.; Ji, Cheng; Kelley, Neil P.; Fu, Wan-Lu; Zhang, Rong

2016-01-01

Contrary to the fast radiation of most metazoans after the end-Permian mass extinction, it is believed that early marine reptiles evolved slowly during the same time interval. However, emerging discoveries of Early Triassic marine reptiles are questioning this traditional view. Here we present an aberrant basal ichthyosauriform with a hitherto unknown body design that suggests a fast radiation of early marine reptiles. The new species is larger than coeval marine reptiles and has an extremely small head and a long tail without a fluke. Its heavily-built body bears flattened and overlapping gastral elements reminiscent of hupehsuchians. A phylogenetic analysis places the new species at the base of ichthyosauriforms, as the sister taxon of Cartorhynchus with which it shares a short snout with rostrally extended nasals. It now appears that ichthyosauriforms evolved rapidly within the first one million years of their evolution, in the Spathian (Early Triassic), and their true diversity has yet to be fully uncovered. Early ichthyosauromorphs quickly became extinct near the Early-Middle Triassic boundary, during the last large environmental perturbation after the end-Permian extinction involving redox fluctuations, sea level changes and volcanism. Marine reptile faunas shifted from ichthyosauromorph-dominated to sauropterygian-dominated composition after the perturbation. PMID:27211319

The evolution of red supergiants to supernovae

NASA Astrophysics Data System (ADS)

Beasor, Emma R.; Davies, Ben

2017-11-01

With red supergiants (RSGs) predicted to end their lives as Type IIP core collapse supernova (CCSN), their behaviour before explosion needs to be fully understood. Mass loss rates govern RSG evolution towards SN and have strong implications on the appearance of the resulting explosion. To study how the mass-loss rates change with the evolution of the star, we have measured the amount of circumstellar material around 19 RSGs in a coeval cluster. Our study has shown that mass loss rates ramp up throughout the lifetime of an RSG, with more evolved stars having mass loss rates a factor of 40 higher than early stage RSGs. Interestingly, we have also found evidence for an increase in circumstellar extinction throughout the RSG lifetime, meaning the most evolved stars are most severely affected. We find that, were the most evolved RSGs in NGC2100 to go SN, this extra extinction would cause the progenitor's initial mass to be underestimated by up to 9M⊙.

Evolution and Extinction Dynamics in Rugged Fitness Landscapes

NASA Astrophysics Data System (ADS)

Sibani, Paolo; Brandt, Michael; Alstrøm, Preben

After an introductory section summarizing the paleontological data and some of their theoretical descriptions, we describe the "reset" model and its (in part analytically soluble) mean field version, which have been briefly introduced in Letters.1,2 Macroevolution is considered as a problem of stochastic dynamics in a system with many competing agents. Evolutionary events (speciations and extinctions) are triggered by fitness records found by random exploration of the agents' fitness landscapes. As a consequence, the average fitness in the system increases logarithmically with time, while the rate of extinction steadily decreases. This non-stationary dynamics is studied by numerical simulations and, in a simpler mean field version, analytically. We also consider the effect of externally added "mass" extinctions. The predictions for various quantities of paleontological interest (life-time distribution, distribution of event sizes and behavior of the rate of extinction) are robust and in good agreement with available data.

Social networks: Evolving graphs with memory dependent edges

NASA Astrophysics Data System (ADS)

Grindrod, Peter; Parsons, Mark

2011-10-01

The plethora of digital communication technologies, and their mass take up, has resulted in a wealth of interest in social network data collection and analysis in recent years. Within many such networks the interactions are transient: thus those networks evolve over time. In this paper we introduce a class of models for such networks using evolving graphs with memory dependent edges, which may appear and disappear according to their recent history. We consider time discrete and time continuous variants of the model. We consider the long term asymptotic behaviour as a function of parameters controlling the memory dependence. In particular we show that such networks may continue evolving forever, or else may quench and become static (containing immortal and/or extinct edges). This depends on the existence or otherwise of certain infinite products and series involving age dependent model parameters. We show how to differentiate between the alternatives based on a finite set of observations. To test these ideas we show how model parameters may be calibrated based on limited samples of time dependent data, and we apply these concepts to three real networks: summary data on mobile phone use from a developing region; online social-business network data from China; and disaggregated mobile phone communications data from a reality mining experiment in the US. In each case we show that there is evidence for memory dependent dynamics, such as that embodied within the class of models proposed here.

The large terrestrial carnivore guild in Quaternary Southeast Asia

NASA Astrophysics Data System (ADS)

Louys, Julien

2014-07-01

Much of Southeast Asia's large terrestrial carnivores appeared, evolved and disappeared from the region for reasons that remain poorly understood. Two of the most significant extinctions are represented by the charismatic Pleistocene megacarnivores Pachycrocuta and Pliocrocuta. Southeast Asia hosts the last populations of these species globally. Their persistence in southern China until the late Pleistocene suggests their extinction was not tied to that of the machairodont cats, which like the rest of the world became extinct sometime in the early Pleistocene in this region. Instead the disappearance of the hyenids is probably related to climate change and deteriorating environmental conditions. There is some evidence that the wolf and domesticated dog first appeared in Southeast Asia, although confirmation of this awaits more detailed fossil records. There does not appear to be a large carnivore guild turnover of the same scale or time as recorded in Europe and Africa, although an extinction event in the late Pleistocene is provisionally recorded. Environmental changes and fluctuating sea levels have had a unique impact on the region's large carnivore guild. Several large carnivores from Java show unique genetic and morphological variations, and this could potentially be related to the connection between Java and the Indochinese mainland sometime during the middle Pleistocene. The effects of islands on the large carnivores are complicated and at times contradictory. Nevertheless, periods of isolation of large carnivores on Java, Sumatra and Borneo from the continent had impacts on both extinctions and speciations, with at least one well documented endemic large carnivore evolving in Sundaland (Sunda clouded leopard). Hunting and deforestation ongoing since the mid- to late Holocene means that many extant members of the large carnivore guild are at high risk of extinction.

Seasonal differences in extinction and colonization drive occupancy dynamics of an imperilled amphibian.

PubMed

Randall, Lea A; Smith, Des H V; Jones, Breana L; Prescott, David R C; Moehrenschlager, Axel

2015-01-01

A detailed understanding of the population dynamics of many amphibian species is lacking despite concerns about declining amphibian biodiversity and abundance. This paper explores temporal patterns of occupancy and underlying extinction and colonization dynamics in a regionally imperiled amphibian species, the Northern leopard frog (Lithobates pipiens) in Alberta. Our study contributes to elucidating regional occupancy dynamics at northern latitudes, where climate extremes likely have a profound effect on seasonal occupancy. The primary advantage of our study is its wide geographic scale (60,000 km2) and the use of repeat visual surveys each spring and summer from 2009-2013. We find that occupancy varied more dramatically between seasons than years, with low spring and higher summer occupancy. Between spring and summer, colonization was high and extinction low; inversely, colonization was low and extinction high over the winter. The dynamics of extinction and colonization are complex, making conservation management challenging. Our results reveal that Northern leopard frog occupancy was constant over the last five years and thus there is no evidence of decline or recovery within our study area. Changes to equilibrium occupancy are most sensitive to increasing colonization in the spring or declining extinction in the summer. Therefore, conservation and management efforts should target actions that are likely to increase spring colonization; this could be achieved through translocations or improving the quality or access to breeding habitat. Because summer occupancy is already high, it may be difficult to improve further. Nevertheless, summer extinction could be reduced by predator control, increasing water quality or hydroperiod of wetlands, or increasing the quality or quantity of summer habitat.

Environmental change makes robust ecological networks fragile

PubMed Central

Strona, Giovanni; Lafferty, Kevin D.

2016-01-01

Complex ecological networks appear robust to primary extinctions, possibly due to consumers' tendency to specialize on dependable (available and persistent) resources. However, modifications to the conditions under which the network has evolved might alter resource dependability. Here, we ask whether adaptation to historical conditions can increase community robustness, and whether such robustness can protect communities from collapse when conditions change. Using artificial life simulations, we first evolved digital consumer-resource networks that we subsequently subjected to rapid environmental change. We then investigated how empirical host–parasite networks would respond to historical, random and expected extinction sequences. In both the cases, networks were far more robust to historical conditions than new ones, suggesting that new environmental challenges, as expected under global change, might collapse otherwise robust natural ecosystems. PMID:27511722

Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection

PubMed Central

2008-01-01

Background The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. Results Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. Conclusion Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction. PMID:18637173

Outbreak and Extinction Dynamics in a Stochastic Ebola Model

NASA Astrophysics Data System (ADS)

Nieddu, Garrett; Bianco, Simone; Billings, Lora; Forgoston, Eric; Kaufman, James

A zoonotic disease is a disease that can be passed between animals and humans. In many cases zoonotic diseases can persist in the animal population even if there are no infections in the human population. In this case we call the infected animal population the reservoir for the disease. Ebola virus disease (EVD) and SARS are both notable examples of such diseases. There is little work devoted to understanding stochastic disease extinction and reintroduction in the presence of a reservoir. Here we build a stochastic model for EVD and explicitly consider the presence of an animal reservoir. Using a master equation approach and a WKB ansatz, we determine the associated Hamiltonian of the system. Hamilton's equations are then used to numerically compute the 12-dimensional optimal path to extinction, which is then used to estimate mean extinction times. We also numerically investigate the behavior of the model for dynamic population size. Our results provide an improved understanding of outbreak and extinction dynamics in diseases like EVD.

Theory of invasion extinction dynamics in minimal food webs

NASA Astrophysics Data System (ADS)

Haerter, Jan O.; Mitarai, Namiko; Sneppen, Kim

2018-02-01

When food webs are exposed to species invasion, secondary extinction cascades may be set off. Although much work has gone into characterizing the structure of food webs, systematic predictions on their evolutionary dynamics are still scarce. Here we present a theoretical framework that predicts extinctions in terms of an alternating sequence of two basic processes: resource depletion by or competitive exclusion between consumers. We first propose a conceptual invasion extinction model (IEM) involving random fitness coefficients. We bolster this IEM by an analytical, recursive procedure for calculating idealized extinction cascades after any species addition and simulate the long-time evolution. Our procedure describes minimal food webs where each species interacts with only a single resource through the generalized Lotka-Volterra equations. For such food webs ex- tinction cascades are determined uniquely and the system always relaxes to a stable steady state. The dynamics and scale invariant species life time resemble the behavior of the IEM, and correctly predict an upper limit for trophic levels as observed in the field.

Theory of invasion extinction dynamics in minimal food webs.

PubMed

Haerter, Jan O; Mitarai, Namiko; Sneppen, Kim

2018-02-01

When food webs are exposed to species invasion, secondary extinction cascades may be set off. Although much work has gone into characterizing the structure of food webs, systematic predictions on their evolutionary dynamics are still scarce. Here we present a theoretical framework that predicts extinctions in terms of an alternating sequence of two basic processes: resource depletion by or competitive exclusion between consumers. We first propose a conceptual invasion extinction model (IEM) involving random fitness coefficients. We bolster this IEM by an analytical, recursive procedure for calculating idealized extinction cascades after any species addition and simulate the long-time evolution. Our procedure describes minimal food webs where each species interacts with only a single resource through the generalized Lotka-Volterra equations. For such food webs ex- tinction cascades are determined uniquely and the system always relaxes to a stable steady state. The dynamics and scale invariant species life time resemble the behavior of the IEM, and correctly predict an upper limit for trophic levels as observed in the field.

Influence of habitat quality, population size, patch size, and connectivity on patch-occupancy dynamics of the middle spotted woodpecker.

PubMed

Robles, Hugo; Ciudad, Carlos

2012-04-01

Despite extensive research on the effects of habitat fragmentation, the ecological mechanisms underlying colonization and extinction processes are poorly known, but knowledge of these mechanisms is essential to understanding the distribution and persistence of populations in fragmented habitats. We examined these mechanisms through multiseason occupancy models that elucidated patch-occupancy dynamics of Middle Spotted Woodpeckers (Dendrocopos medius) in northwestern Spain. The number of occupied patches was relatively stable from 2000 to 2010 (15-24% of 101 patches occupied every year) because extinction was balanced by recolonization. Larger and higher quality patches (i.e., higher density of oaks >37 cm dbh [diameter at breast height]) were more likely to be occupied. Habitat quality (i.e., density of large oaks) explained more variation in patch colonization and extinction than did patch size and connectivity, which were both weakly associated with probabilities of turnover. Patches of higher quality were more likely to be colonized than patches of lower quality. Populations in high-quality patches were less likely to become extinct. In addition, extinction in a patch was strongly associated with local population size but not with patch size, which means the latter may not be a good surrogate of population size in assessments of extinction probability. Our results suggest that habitat quality may be a primary driver of patch-occupancy dynamics and may increase the accuracy of models of population survival. We encourage comparisons of competing models that assess occupancy, colonization, and extinction probabilities in a single analytical framework (e.g., dynamic occupancy models) so as to shed light on the association of habitat quality and patch geometry with colonization and extinction processes in different settings and species. ©2012 Society for Conservation Biology.

The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

PubMed Central

Yang, Guan-Dong; Agapow, Paul-Michael

2017-01-01

The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors. PMID:28644846

Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss

NASA Technical Reports Server (NTRS)

Lazaro, Ester; Escarmis, Cristina; Perez-Mercader, Juan; Manrubia, Susanna C.; Domingo, Esteban

2003-01-01

RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern.

Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

PubMed Central

Quandt, Erik M; Gollihar, Jimmy; Blount, Zachary D; Ellington, Andrew D; Georgiou, George; Barrick, Jeffrey E

2015-01-01

Evolutionary innovations that enable organisms to colonize new ecological niches are rare compared to gradual evolutionary changes in existing traits. We discovered that key mutations in the gltA gene, which encodes citrate synthase (CS), occurred both before and after Escherichia coli gained the ability to grow aerobically on citrate (Cit+ phenotype) during the Lenski long-term evolution experiment. The first gltA mutation, which increases CS activity by disrupting NADH-inhibition of this enzyme, is beneficial for growth on the acetate and contributed to preserving the rudimentary Cit+ trait from extinction when it first evolved. However, after Cit+ was refined by further mutations, this potentiating gltA mutation became deleterious to fitness. A second wave of beneficial gltA mutations then evolved that reduced CS activity to below the ancestral level. Thus, dynamic reorganization of central metabolism made colonizing this new nutrient niche contingent on both co-opting and overcoming a history of prior adaptation. DOI: http://dx.doi.org/10.7554/eLife.09696.001 PMID:26465114

Character convergence under competition for nutritionally essential resources.

PubMed

Fox, Jeremy W; Vasseur, David A

2008-11-01

Resource competition is thought to drive divergence in resource use traits (character displacement) by generating selection favoring individuals able to use resources unavailable to others. However, this picture assumes nutritionally substitutable resources (e.g., different prey species). When species compete for nutritionally essential resources (e.g., different nutrients), theory predicts that selection drives character convergence. We used models of two species competing for two essential resources to address several issues not considered by existing theory. The models incorporated either slow evolutionary change in resource use traits or fast physiological or behavioral change. We report four major results. First, competition always generates character convergence, but differences in resource requirements prevent competitors from evolving identical resource use traits. Second, character convergence promotes coexistence. Competing species always attain resource use traits that allow coexistence, and adaptive trait change stabilizes the ecological equilibrium. In contrast, adaptation in allopatry never preadapts species to coexist in sympatry. Third, feedbacks between ecological dynamics and trait dynamics lead to surprising dynamical trajectories such as transient divergence in resource use traits followed by subsequent convergence. Fourth, under sufficiently slow trait change, ecological dynamics often drive one of the competitors to near extinction, which would prevent realization of long-term character convergence in practice.

Evolution and extinction in the marine realm: some constraints imposed by phytoplankton

NASA Technical Reports Server (NTRS)

Knoll, A. H.

1989-01-01

The organic and mineralized remains of planktonic algae provide a rich record of microplankton evolution extending over nearly half of the preserved geological record. In general, Phanerozoic patterns of phytoplankton radiation and extinction parallel those documented for skeletonized marine invertebrates, both augmenting and constraining thought about evolution in the oceans. Rapidly increasing knowledge of Proterozoic plankton is making possible the recognition of additional episodes of diversification and extinction that antedate the Ediacaran radiation of macroscopic animals. In contrast to earlier phytoplankton history, the late Mesozoic and Cainozoic record is documented in sufficient detail to constrain theories of mass extinction in more than a general way. Broad patterns of diversity change in planktonic algae show similarities across the Cretaceous-Tertiary and Eocene-Oligocene boundaries, but detailed comparisons of origination and extinction rates in calcareous nannoplankton, as well as other algae and skeletonized protozoans, suggest that the two episodes were quite distinct. Common causation appears unlikely, casting doubt on monolithic theories of mass extinction, whether periodic or not. Studies of mass extinction highlight a broader class of insights that paleontologists can contribute to evolutionary biology: the evaluation of evolutionary change in the context of evolving Earth-surface environments.

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

USGS Publications Warehouse

Kennedy, Christina M.; Campbell Grant, Evan H.; Neel, Maile C.; Fagan, William F.; Marpa, Peter P.

2011-01-01

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical nsectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban evelopment, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

Dynamics Analysis of Anti-predator Model on Intermediate Predator With Ratio Dependent Functional Responses

NASA Astrophysics Data System (ADS)

Savitri, D.

2018-01-01

This articel discusses a predator prey model with anti-predator on intermediate predator using ratio dependent functional responses. Dynamical analysis performed on the model includes determination of equilibrium point, stability and simulation. Three kinds of equilibrium points have been discussed, namely the extinction of prey point, the extinction of intermediate predator point and the extinction of predator point are exists under certain conditions. It can be shown that the result of numerical simulations are in accordance with analitical results

Modeling Selection and Extinction Mechanisms of Biological Systems

NASA Astrophysics Data System (ADS)

Amirjanov, Adil

In this paper, the behavior of a genetic algorithm is modeled to enhance its applicability as a modeling tool of biological systems. A new description model for selection mechanism is introduced which operates on a portion of individuals of population. The extinction and recolonization mechanism is modeled, and solving the dynamics analytically shows that the genetic drift in the population with extinction/recolonization is doubled. The mathematical analysis of the interaction between selection and extinction/recolonization processes is carried out to assess the dynamics of motion of the macroscopic statistical properties of population. Computer simulations confirm that the theoretical predictions of described models are in good approximations. A mathematical model of GA dynamics was also examined, which describes the anti-predator vigilance in an animal group with respect to a known analytical solution of the problem, and showed a good agreement between them to find the evolutionarily stable strategies.

Dynamics of an eco-epidemiological model with saturated incidence rate

NASA Astrophysics Data System (ADS)

Suryanto, Agus

2017-03-01

In this paper we study the effect of prey infection on the modified Leslie-Gower predator-prey model with saturated incidence rate. The model will be analyzed dynamically to find the equilibria and their existence conditions as well as their local stability conditions. It is found that there are six type of equilibria, namely the extinction of both prey and predator point, the extinction of infective prey and predator point, the extinction of predator point, the extinction of prey point, the extinction of infective prey point and the interior point. The first four equilibrium points are always unstable, while the last two equilibria are conditionally stable. We also find that the system undergoes Hopf bifurcation around the interior point which is controlled by the rate of infection. To illustrate our analytical results, we show some numerical results.

Local extinction and turnover rates at the edge and interior of species' ranges

USGS Publications Warehouse

Doherty, P.F.; Boulinier, T.; James., D.

2003-01-01

One hypothesis for the maintenance of the edge of a species' range suggests that more central (and abundant) populations are relatively stable and edge populations are less stable with increased local extinction and turnover rates. To date, estimates of such metrics are equivocal due to design and analysis flaws. Apparent increased estimates of extinction and turnover rates at the edge of range, versus the interior, could be a function of decreased detection probabilities alone, and not of a biological process. We estimated extinction and turnover rates for species at the interiors and edges of their ranges using an approach which incorporates potential heterogeneity in species detection probabilities. Extinction rates were higher at the edges (0.17 ?? 0.03 []) than in the interiors (0.04 ?? 0.01), as was turnover. Without taking the probability of detection into account these differences would be artificially magnified. Knowledge of extinction and turnover rates is essential in furthering our understanding of range dynamics, and in directing conservation efforts. This study further illustrates the practical application of methods proposed recently for estimating extinction rates and other community dynamic parameters.

Local extinction and turnover rates at the edge and interior of species' ranges

USGS Publications Warehouse

Doherty, P.F.; Boulinier, T.; Nichols, J.D.

2003-01-01

One hypothesis for the maintenance of the edge of a species' range suggests that more central (and abundant) populations are relatively stable and edge populations are less stable with increased local extinction and turnover rates. To date, estimates of such metrics are equivocal due to design and analysis flaws. Apparent increased estimates of extinction and turnover rates at the edge of range, versus the interior, could be a function of decreased detection probabilities alone, and not of a biological process. We estimated extinction and turnover rates for species at the interiors and edges of their ranges using an approach which incorporates potential heterogeneity in species detection probabilities. Extinction rates were higher at the edges (0.17 ' 0.03 [SE]) than in the interiors (0.04 ' 0.01), as was turnover. Without taking the probability of detection into account these differences would be artificially magnified. Knowledge of extinction and turnover rates is essential in furthering our understanding of range dynamics, and in directing conservation efforts. This study further illustrates the practical application of methods proposed recently for estimating extinction rates and other community dynamic parameters.

Different evolution dynamics of vector solitons depending on their polarization states

NASA Astrophysics Data System (ADS)

Chen, Wei-Cheng; Chen, Guo-Jie

2014-03-01

There are three types of temporal evolution dynamics of vector solitons observed in a ring fiber laser with a semiconductor saturable absorption mirror (SESAM) as a mode-locker. It is found that the polarization property of vector solitons is an important factor for achieving different evolution dynamics. The vector soliton with a uniform polarization state across the whole pulse profile and zero polarization extinction ratio operates at a fundamental repetition rate with a single pulse profile. The elliptically polarized vector soliton with a larger polarization extinction ratio exhibits a harmonic pulse train. The soliton bunching with multi-peak structures exists between the above two states and shows elliptical polarization with a small polarization extinction ratio.

Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations

PubMed Central

Dey, Snigdhadip; Joshi, Amitabh

2013-01-01

Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways. PMID:23470546

Resurrection of DNA Function In Vivo from an Extinct Genome

PubMed Central

Pask, Andrew J.; Behringer, Richard R.; Renfree, Marilyn B.

2008-01-01

There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity. PMID:18493600

Conservation Risks: When Will Rhinos be Extinct?

PubMed

Haas, Timothy C; Ferreira, Sam M

2016-08-01

We develop a risk intelligence system for biodiversity enterprises. Such enterprises depend on a supply of endangered species for their revenue. Many of these enterprises, however, cannot purchase a supply of this resource and are largely unable to secure the resource against theft in the form of poaching. Because replacements are not available once a species becomes extinct, insurance products are not available to reduce the risk exposure of these enterprises to an extinction event. For many species, the dynamics of anthropogenic impacts driven by economic as well as noneconomic values of associated wildlife products along with their ecological stressors can help meaningfully predict extinction risks. We develop an agent/individual-based economic-ecological model that captures these effects and apply it to the case of South African rhinos. Our model uses observed rhino dynamics and poaching statistics. It seeks to predict rhino extinction under the present scenario. This scenario has no legal horn trade, but allows live African rhino trade and legal hunting. Present rhino populations are small and threatened by a rising onslaught of poaching. This present scenario and associated dynamics predicts continued decline in rhino population size with accelerated extinction risks of rhinos by 2036. Our model supports the computation of extinction risks at any future time point. This capability can be used to evaluate the effectiveness of proposed conservation strategies at reducing a species' extinction risk. Models used to compute risk predictions, however, need to be statistically estimated. We point out that statistically fitting such models to observations will involve massive numbers of observations on consumer behavior and time-stamped location observations on thousands of animals. Finally, we propose Big Data algorithms to perform such estimates and to interpret the fitted model's output.

Consequences of biodiversity loss diverge from expectation due to post-extinction compensatory responses

NASA Astrophysics Data System (ADS)

Thomsen, Matthias S.; Garcia, Clement; Bolam, Stefan G.; Parker, Ruth; Godbold, Jasmin A.; Solan, Martin

2017-03-01

Consensus has been reached that global biodiversity loss impairs ecosystem functioning and the sustainability of services beneficial to humanity. However, the ecosystem consequences of extinction in natural communities are moderated by compensatory species dynamics, yet these processes are rarely accounted for in impact assessments and seldom considered in conservation programmes. Here, we use marine invertebrate communities to parameterise numerical models of sediment bioturbation - a key mediator of biogeochemical cycling - to determine whether post-extinction compensatory mechanisms alter biodiversity-ecosystem function relations following non-random extinctions. We find that compensatory dynamics lead to trajectories of sediment mixing that diverge from those without compensation, and that the form, magnitude and variance of each probabilistic distribution is highly influenced by the type of compensation and the functional composition of surviving species. Our findings indicate that the generalized biodiversity-function relation curve, as derived from multiple empirical investigations of random species loss, is unlikely to yield representative predictions for ecosystem properties in natural systems because the influence of post-extinction community dynamics are under-represented. Recognition of this problem is fundamental to management and conservation efforts, and will be necessary to ensure future plans and adaptation strategies minimize the adverse impacts of the biodiversity crisis.

Bone microstructure and the evolution of growth patterns in Permo-Triassic therocephalians (Amniota, Therapsida) of South Africa

PubMed Central

Botha-Brink, Jennifer

2014-01-01

Therocephalians were a speciose clade of nonmammalian therapsids whose ecological diversity and survivorship of the end-Permian mass extinction offer the potential to investigate the evolution of growth patterns across the clade and their underlying influences on post-extinction body size reductions, or ‘Lilliput effects’. We present a phylogenetic survey of limb bone histology and growth patterns in therocephalians from the Middle Permian through Middle Triassic of the Karoo Basin, South Africa. Histologic sections were prepared from 80 limb bones representing 11 genera of therocephalians. Histologic indicators of skeletal growth, including cortical vascularity (%CV) and mean primary osteon diameters (POD), were evaluated in a phylogenetic framework and assessed for correlations with other biologically significant variables (e.g., size and robusticity). Changes in %CV and POD correlated strongly with evolutionary changes in body size (i.e., smaller-bodied descendants tended to have lower %CV than their larger-bodied ancestors across the tree). Bone wall thickness tended to be high in early therocephalians and lower in the gracile-limbed baurioids, but showed no general correlation with cross-sectional area or degree of vascularity (and, thus, growth). Clade-level patterns, however, deviated from previously studied within-lineage patterns. For example, Moschorhinus, one of few therapsid genera to have survived the extinction boundary, demonstrated higher %CV in the Triassic than in the Permian despite its smaller size in the extinction aftermath. Results support a synergistic model of size reductions for Triassic therocephalians, influenced both by within-lineage heterochronic shifts in survivor taxa (as reported in Moschorhinus and the dicynodont Lystrosaurus) and phylogenetically inferred survival of small-bodied taxa that had evolved short growth durations (e.g., baurioids). These findings mirror the multi-causal Lilliput patterns described in marine faunas, but contrast with skeletochronologic studies that suggest slow, prolonged shell secretion over several years in marine benthos. Applications of phylogenetic comparative methods to new histologic data will continue to improve our understanding of the evolutionary dynamics of growth and body size shifts during mass extinctions and recoveries. PMID:24765566

Unique Cellular Organization in the Oldest Root Meristem.

PubMed

Hetherington, Alexander J; Dubrovsky, Joseph G; Dolan, Liam

2016-06-20

Roots and shoots of plant bodies develop from meristems-cell populations that self-renew and produce cells that undergo differentiation-located at the apices of axes [1].The oldest preserved root apices in which cellular anatomy can be imaged are found in nodules of permineralized fossil soils called coal balls [2], which formed in the Carboniferous coal swamp forests over 300 million years ago [3-9]. However, no fossil root apices described to date were actively growing at the time of preservation [3-10]. Because the cellular organization of meristems changes when root growth stops, it has been impossible to compare cellular dynamics as stem cells transition to differentiated cells in extinct and extant taxa [11]. We predicted that meristems of actively growing roots would be preserved in coal balls. Here we report the discovery of the first fossilized remains of an actively growing root meristem from permineralized Carboniferous soil with detail of the stem cells and differentiating cells preserved. The cellular organization of the meristem is unique. The position of the Körper-Kappe boundary, discrete root cap, and presence of many anticlinal cell divisions within a broad promeristem distinguish it from all other known root meristems. This discovery is important because it demonstrates that the same general cellular dynamics are conserved between the oldest extinct and extant root meristems. However, its unique cellular organization demonstrates that extant root meristem organization and development represents only a subset of the diversity that has existed since roots first evolved. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Extinction in neutrally stable stochastic Lotka-Volterra models

NASA Astrophysics Data System (ADS)

Dobrinevski, Alexander; Frey, Erwin

2012-05-01

Populations of competing biological species exhibit a fascinating interplay between the nonlinear dynamics of evolutionary selection forces and random fluctuations arising from the stochastic nature of the interactions. The processes leading to extinction of species, whose understanding is a key component in the study of evolution and biodiversity, are influenced by both of these factors. Here, we investigate a class of stochastic population dynamics models based on generalized Lotka-Volterra systems. In the case of neutral stability of the underlying deterministic model, the impact of intrinsic noise on the survival of species is dramatic: It destroys coexistence of interacting species on a time scale proportional to the population size. We introduce a new method based on stochastic averaging which allows one to understand this extinction process quantitatively by reduction to a lower-dimensional effective dynamics. This is performed analytically for two highly symmetrical models and can be generalized numerically to more complex situations. The extinction probability distributions and other quantities of interest we obtain show excellent agreement with simulations.

Extinction in neutrally stable stochastic Lotka-Volterra models.

PubMed

Dobrinevski, Alexander; Frey, Erwin

2012-05-01

Populations of competing biological species exhibit a fascinating interplay between the nonlinear dynamics of evolutionary selection forces and random fluctuations arising from the stochastic nature of the interactions. The processes leading to extinction of species, whose understanding is a key component in the study of evolution and biodiversity, are influenced by both of these factors. Here, we investigate a class of stochastic population dynamics models based on generalized Lotka-Volterra systems. In the case of neutral stability of the underlying deterministic model, the impact of intrinsic noise on the survival of species is dramatic: It destroys coexistence of interacting species on a time scale proportional to the population size. We introduce a new method based on stochastic averaging which allows one to understand this extinction process quantitatively by reduction to a lower-dimensional effective dynamics. This is performed analytically for two highly symmetrical models and can be generalized numerically to more complex situations. The extinction probability distributions and other quantities of interest we obtain show excellent agreement with simulations.

The last diadectomorph sheds light on Late Palaeozoic tetrapod biogeography.

PubMed

Liu, Jun; Bever, G S

2015-05-01

Diadectomorpha is a clade of Late Palaeozoic vertebrates widely recognized as the sister group of crown-group Amniota and the first tetrapod lineage to evolve high-fibre herbivory. Despite their evolutionary importance, diadectomorphs are restricted stratigraphically and geographically, with all records being from the Upper Carboniferous and Lower Permian of North America and Germany. We describe a new diadectomorph, Alveusdectes fenestralis, based on a partial skull from the Upper Permian of China. The new species exhibits the derived mechanism for herbivory and is recovered phylogenetically as a deeply nested diadectid. Approximately 16 Myr younger than any other diadectomorph, Alveusdectes is the product of at least a 46 Myr ghost lineage. How much of this time was probably spent in Russia and/or central Asia will remain unclear until a specimen is described that subdivides this cryptic history, but the lineage assuredly crossed this region before entering the relatively isolated continent of North China. The discovery of Alveusdectes raises important questions regarding diadectomorph extinction dynamics including what, if any, ecological factors limited the diversity of this group in eastern Pangea. It also suggests that increased sampling in Asia will likely significantly affect our views of clade and faunal insularity leading up to the Permo-Triassic extinction. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The last diadectomorph sheds light on Late Palaeozoic tetrapod biogeography

PubMed Central

Liu, Jun; Bever, G. S.

2015-01-01

Diadectomorpha is a clade of Late Palaeozoic vertebrates widely recognized as the sister group of crown-group Amniota and the first tetrapod lineage to evolve high-fibre herbivory. Despite their evolutionary importance, diadectomorphs are restricted stratigraphically and geographically, with all records being from the Upper Carboniferous and Lower Permian of North America and Germany. We describe a new diadectomorph, Alveusdectes fenestralis, based on a partial skull from the Upper Permian of China. The new species exhibits the derived mechanism for herbivory and is recovered phylogenetically as a deeply nested diadectid. Approximately 16 Myr younger than any other diadectomorph, Alveusdectes is the product of at least a 46 Myr ghost lineage. How much of this time was probably spent in Russia and/or central Asia will remain unclear until a specimen is described that subdivides this cryptic history, but the lineage assuredly crossed this region before entering the relatively isolated continent of North China. The discovery of Alveusdectes raises important questions regarding diadectomorph extinction dynamics including what, if any, ecological factors limited the diversity of this group in eastern Pangea. It also suggests that increased sampling in Asia will likely significantly affect our views of clade and faunal insularity leading up to the Permo-Triassic extinction. PMID:25948572

Diversifying evolution of competitiveness.

PubMed

Baldauf, Sebastian A; Engqvist, Leif; Weissing, Franz J

2014-10-29

In many species, individuals express phenotypic characteristics that enhance their competitiveness, that is, the ability to acquire resources in competition with others. Moreover, the degree of competitiveness varies considerably across individuals and in time. By means of an evolutionary model, we provide an explanation for this finding. We make the assumption that investment into competitiveness enhances the probability to acquire a high-quality resource, but at the same time reduces the ability of exploiting acquired resources with maximal efficiency. The model reveals that under a broad range of conditions competitiveness either converges to a polymorphic state, where individuals differing in competitive ability stably coexist, or is subject to perpetual transitions between periods of high and low competitiveness. The dynamics becomes even more complex if females can evolve preferences for (or against) competitive males. In extreme cases, such preferences can even drive the population to extinction.

Using step width to compare locomotor biomechanics between extinct, non-avian theropod dinosaurs and modern obligate bipeds.

PubMed

Bishop, P J; Clemente, C J; Weems, R E; Graham, D F; Lamas, L P; Hutchinson, J R; Rubenson, J; Wilson, R S; Hocknull, S A; Barrett, R S; Lloyd, D G

2017-07-01

How extinct, non-avian theropod dinosaurs locomoted is a subject of considerable interest, as is the manner in which it evolved on the line leading to birds. Fossil footprints provide the most direct evidence for answering these questions. In this study, step width-the mediolateral (transverse) distance between successive footfalls-was investigated with respect to speed (stride length) in non-avian theropod trackways of Late Triassic age. Comparable kinematic data were also collected for humans and 11 species of ground-dwelling birds. Permutation tests of the slope on a plot of step width against stride length showed that step width decreased continuously with increasing speed in the extinct theropods ( p < 0.001), as well as the five tallest bird species studied ( p < 0.01). Humans, by contrast, showed an abrupt decrease in step width at the walk-run transition. In the modern bipeds, these patterns reflect the use of either a discontinuous locomotor repertoire, characterized by distinct gaits (humans), or a continuous locomotor repertoire, where walking smoothly transitions into running (birds). The non-avian theropods are consequently inferred to have had a continuous locomotor repertoire, possibly including grounded running. Thus, features that characterize avian terrestrial locomotion had begun to evolve early in theropod history. © 2017 The Author(s).

Adaptive Dynamics, Control, and Extinction in Networked Populations

DTIC Science & Technology

2015-07-09

network geometries. From the pre-history of paths that go extinct, a density function is created from the prehistory of these paths, and a clear local...density plots of Fig. 3b. Using the IAMM to compute the most probable path and comparing it to the prehistory of extinction events on stochastic networks

Five palaeobiological laws needed to understand the evolution of the living biota.

PubMed

Marshall, Charles R

2017-05-23

The foundations of several disciplines can be expressed as simple quantitative laws, for example, Newton's laws or the laws of thermodynamics. Here I present five laws derived from fossil data that describe the relationships among species extinction and longevity, species richness, origination rates, extinction rates and diversification. These statements of our palaeobiological knowledge constitute a dimension largely hidden from view when studying the living biota, which are nonetheless crucial to the study of evolution and ecology even for groups with poor or non-existent fossil records. These laws encapsulate: the critical fact of extinction; that species are typically geologically short-lived, and thus that the number of extinct species typically dwarfs the number of living species; that extinction and origination rates typically have similar magnitudes; and, that significant extinction makes it difficult to infer much about a clade's early history or its current diversity dynamics from the living biota alone. Although important strides are being made to integrate these core palaeontological findings into our analysis of the living biota, this knowledge needs to be incorporated more widely if we are to understand their evolutionary dynamics.

An analytical prediction of the oscillation and extinction thresholds of a clarinet

NASA Astrophysics Data System (ADS)

Dalmont, Jean-Pierre; Gilbert, Joël; Kergomard, Jean; Ollivier, Sébastien

2005-11-01

This paper investigates the dynamic range of the clarinet from the oscillation threshold to the extinction at high pressure level. The use of an elementary model for the reed-mouthpiece valve effect combined with a simplified model of the pipe assuming frequency independent losses (Raman's model) allows an analytical calculation of the oscillations and their stability analysis. The different thresholds are shown to depend on parameters related to embouchure parameters and to the absorption coefficient in the pipe. Their values determine the dynamic range of the fundamental oscillations and the bifurcation scheme at the extinction.

The Effect of Size and Ecology on Extinction Susceptibility

NASA Astrophysics Data System (ADS)

Huynh, C.; Yuan, A.; Heim, N.; Payne, J.

2015-12-01

Although life on Earth first emerged as prokaryotic organisms, it eventually evolved into billions of different species. However, extinctions on Earth, especially the five mass extinctions, have decimated species. So what leads to a species survival or demise during a mass extinction? Are certain species more susceptible to extinctions based on their size and ecology? For this project, we focused on the data of marine animals. To examine the impact of size and ecology on a species's likelihood of survival, we compared the sizes and ecologies of the survivors and victims of the five mass extinctions. The ecology, or life mode, of a genus consists of the combination of tiering, motility, and feeding mechanism. Tiering refers to the animal's typical location in the water column and sediments, motility refers to its ability to move, and feeding mechanism describes the way the organism eats; together, they describe the animal's behavior. We analyzed the effect of ecology on survival using logistic regression, which compares life mode to the success or failure of a genus during each mass extinction interval. For organism size, we found the extinct organisms' mean size (both volume and length) and compared it with the average size of survivors on a graph. Our results show that while surviving genera of mass extinctions tended to be slightly larger than those that went extinct, there was no significant difference. Even though the Permian (Changhsingian) and Triassic (Rhaetian) extinctions had larger surviving species, likewise the difference was small. Ecology had a more obvious impact on the likelihood of survival; fast-moving, predatory pelagic organisms were the most likely to go extinct, while sedentary, infaunal suspension feeders had the greatest chances of survival. Overall, ecology played a greater role than size in determining the survival of a species. With this information, we can use ecology to predict which species would survive future extinctions.

Extinction Risk and Diversification Are Linked in a Plant Biodiversity Hotspot

PubMed Central

Davies, T. Jonathan; Smith, Gideon F.; Bellstedt, Dirk U.; Boatwright, James S.; Bytebier, Benny; Cowling, Richard M.; Forest, Félix; Harmon, Luke J.; Muasya, A. Muthama; Schrire, Brian D.; Steenkamp, Yolande; van der Bank, Michelle; Savolainen, Vincent

2011-01-01

It is widely recognized that we are entering an extinction event on a scale approaching the mass extinctions seen in the fossil record. Present-day rates of extinction are estimated to be several orders of magnitude greater than background rates and are projected to increase further if current trends continue. In vertebrates, species traits, such as body size, fecundity, and geographic range, are important predictors of vulnerability. Although plants are the basis for life on Earth, our knowledge of plant extinctions and vulnerabilities is lagging. Here, we disentangle the underlying drivers of extinction risk in plants, focusing on the Cape of South Africa, a global biodiversity hotspot. By comparing Red List data for the British and South African floras, we demonstrate that the taxonomic distribution of extinction risk differs significantly between regions, inconsistent with a simple, trait-based model of extinction. Using a comprehensive phylogenetic tree for the Cape, we reveal a phylogenetic signal in the distribution of plant extinction risks but show that the most threatened species cluster within short branches at the tips of the phylogeny—opposite to trends in mammals. From analyzing the distribution of threatened species across 11 exemplar clades, we suggest that mode of speciation best explains the unusual phylogenetic structure of extinction risks in plants of the Cape. Our results demonstrate that explanations for elevated extinction risk in plants of the Cape flora differ dramatically from those recognized for vertebrates. In the Cape, extinction risk is higher for young and fast-evolving plant lineages and cannot be explained by correlations with simple biological traits. Critically, we find that the most vulnerable plant species are nonetheless marching towards extinction at a more rapid pace but, surprisingly, independently from anthropogenic effects. Our results have important implications for conservation priorities and cast doubts on the utility of current Red List criteria for plants in regions such as the Cape, where speciation has been rapid, if our aim is to maximize the preservation of the tree-of-life. PMID:21629678

Extinction risk and eco-evolutionary dynamics in a variable environment with increasing frequency of extreme events

PubMed Central

Vincenzi, Simone

2014-01-01

One of the most dramatic consequences of climate change will be the intensification and increased frequency of extreme events. I used numerical simulations to understand and predict the consequences of directional trend (i.e. mean state) and increased variability of a climate variable (e.g. temperature), increased probability of occurrence of point extreme events (e.g. floods), selection pressure and effect size of mutations on a quantitative trait determining individual fitness, as well as the their effects on the population and genetic dynamics of a population of moderate size. The interaction among climate trend, variability and probability of point extremes had a minor effect on risk of extinction, time to extinction and distribution of the trait after accounting for their independent effects. The survival chances of a population strongly and linearly decreased with increasing strength of selection, as well as with increasing climate trend and variability. Mutation amplitude had no effects on extinction risk, time to extinction or genetic adaptation to the new climate. Climate trend and strength of selection largely determined the shift of the mean phenotype in the population. The extinction or persistence of the populations in an ‘extinction window’ of 10 years was well predicted by a simple model including mean population size and mean genetic variance over a 10-year time frame preceding the ‘extinction window’, although genetic variance had a smaller role than population size in predicting contemporary risk of extinction. PMID:24920116

Reconstructing past ecological networks: the reconfiguration of seed-dispersal interactions after megafaunal extinction.

PubMed

Pires, Mathias M; Galetti, Mauro; Donatti, Camila I; Pizo, Marco A; Dirzo, Rodolfo; Guimarães, Paulo R

2014-08-01

The late Quaternary megafaunal extinction impacted ecological communities worldwide, and affected key ecological processes such as seed dispersal. The traits of several species of large-seeded plants are thought to have evolved in response to interactions with extinct megafauna, but how these extinctions affected the organization of interactions in seed-dispersal systems is poorly understood. Here, we combined ecological and paleontological data and network analyses to investigate how the structure of a species-rich seed-dispersal network could have changed from the Pleistocene to the present and examine the possible consequences of such changes. Our results indicate that the seed-dispersal network was organized into modules across the different time periods but has been reconfigured in different ways over time. The episode of megafaunal extinction and the arrival of humans changed how seed dispersers were distributed among network modules. However, the recent introduction of livestock into the seed-dispersal system partially restored the original network organization by strengthening the modular configuration. Moreover, after megafaunal extinctions, introduced species and some smaller native mammals became key components for the structure of the seed-dispersal network. We hypothesize that such changes in network structure affected both animal and plant assemblages, potentially contributing to the shaping of modern ecological communities. The ongoing extinction of key large vertebrates will lead to a variety of context-dependent rearranged ecological networks, most certainly affecting ecological and evolutionary processes.

Pathways to extinction: beyond the error threshold.

PubMed

Manrubia, Susanna C; Domingo, Esteban; Lázaro, Ester

2010-06-27

Since the introduction of the quasispecies and the error catastrophe concepts for molecular evolution by Eigen and their subsequent application to viral populations, increased mutagenesis has become a common strategy to cause the extinction of viral infectivity. Nevertheless, the high complexity of virus populations has shown that viral extinction can occur through several other pathways apart from crossing an error threshold. Increases in the mutation rate enhance the appearance of defective forms and promote the selection of mechanisms that are able to counteract the accelerated appearance of mutations. Current models of viral evolution take into account more realistic scenarios that consider compensatory and lethal mutations, a highly redundant genotype-to-phenotype map, rough fitness landscapes relating phenotype and fitness, and where phenotype is described as a set of interdependent traits. Further, viral populations cannot be understood without specifying the characteristics of the environment where they evolve and adapt. Altogether, it turns out that the pathways through which viral quasispecies go extinct are multiple and diverse.

Evolving learning rules and emergence of cooperation in spatial prisoner's dilemma.

PubMed

Moyano, Luis G; Sánchez, Angel

2009-07-07

In the evolutionary Prisoner's dilemma (PD) game, agents play with each other and update their strategies in every generation according to some microscopic dynamical rule. In its spatial version, agents do not play with every other but, instead, interact only with their neighbours, thus mimicking the existing of a social or contact network that defines who interacts with whom. In this work, we explore evolutionary, spatial PD systems consisting of two types of agents, each with a certain update (reproduction, learning) rule. We investigate two different scenarios: in the first case, update rules remain fixed for the entire evolution of the system; in the second case, agents update both strategy and update rule in every generation. We show that in a well-mixed population the evolutionary outcome is always full defection. We subsequently focus on two-strategy competition with nearest-neighbour interactions on the contact network and synchronised update of strategies. Our results show that, for an important range of the parameters of the game, the final state of the system is largely different from that arising from the usual setup of a single, fixed dynamical rule. Furthermore, the results are also very different if update rules are fixed or evolve with the strategies. In these respect, we have studied representative update rules, finding that some of them may become extinct while others prevail. We describe the new and rich variety of final outcomes that arise from this co-evolutionary dynamics. We include examples of other neighbourhoods and asynchronous updating that confirm the robustness of our conclusions. Our results pave the way to an evolutionary rationale for modelling social interactions through game theory with a preferred set of update rules.

To adapt or go extinct? The fate of megafaunal palm fruits under past global change.

PubMed

Onstein, Renske E; Baker, William J; Couvreur, Thomas L P; Faurby, Søren; Herrera-Alsina, Leonel; Svenning, Jens-Christian; Kissling, W Daniel

2018-06-13

Past global change may have forced animal-dispersed plants with megafaunal fruits to adapt or go extinct, but these processes have remained unexplored at broad spatio-temporal scales. Here, we combine phylogenetic, distributional and fruit size data for more than 2500 palm (Arecaceae) species in a time-slice diversification analysis to quantify how extinction and adaptation have changed over deep time. Our results indicate that extinction rates of palms with megafaunal fruits have increased in the New World since the onset of the Quaternary (2.6 million years ago). In contrast, Old World palms show a Quaternary increase in transition rates towards evolving small fruits from megafaunal fruits. We suggest that Quaternary climate oscillations and concurrent habitat fragmentation and defaunation of megafaunal frugivores in the New World have reduced seed dispersal distances and geographical ranges of palms with megafaunal fruits, resulting in their extinction. The increasing adaptation to smaller fruits in the Old World could reflect selection for seed dispersal by ocean-crossing frugivores (e.g. medium-sized birds and bats) to colonize Indo-Pacific islands against a background of Quaternary sea-level fluctuations. Our macro-evolutionary results suggest that megafaunal fruits are increasingly being lost from tropical ecosystems, either due to extinctions or by adapting to smaller fruit sizes. © 2018 The Authors.

To adapt or go extinct? The fate of megafaunal palm fruits under past global change

PubMed Central

2018-01-01

Past global change may have forced animal-dispersed plants with megafaunal fruits to adapt or go extinct, but these processes have remained unexplored at broad spatio-temporal scales. Here, we combine phylogenetic, distributional and fruit size data for more than 2500 palm (Arecaceae) species in a time-slice diversification analysis to quantify how extinction and adaptation have changed over deep time. Our results indicate that extinction rates of palms with megafaunal fruits have increased in the New World since the onset of the Quaternary (2.6 million years ago). In contrast, Old World palms show a Quaternary increase in transition rates towards evolving small fruits from megafaunal fruits. We suggest that Quaternary climate oscillations and concurrent habitat fragmentation and defaunation of megafaunal frugivores in the New World have reduced seed dispersal distances and geographical ranges of palms with megafaunal fruits, resulting in their extinction. The increasing adaptation to smaller fruits in the Old World could reflect selection for seed dispersal by ocean-crossing frugivores (e.g. medium-sized birds and bats) to colonize Indo-Pacific islands against a background of Quaternary sea-level fluctuations. Our macro-evolutionary results suggest that megafaunal fruits are increasingly being lost from tropical ecosystems, either due to extinctions or by adapting to smaller fruit sizes. PMID:29899077

Ecological consequences of Late Quaternary extinctions of megafauna

PubMed Central

Johnson, C.N.

2009-01-01

Abstract Large herbivorous vertebrates have strong interactions with vegetation, affecting the structure, composition and dynamics of plant communities in many ways. Living large herbivores are a small remnant of the assemblages of giants that existed in most terrestrial ecosystems 50 000 years ago. The extinction of so many large herbivores may well have triggered large changes in plant communities. In several parts of the world, palaeoecological studies suggest that extinct megafauna once maintained vegetation openness, and in wooded landscapes created mosaics of different structural types of vegetation with high habitat and species diversity. Following megafaunal extinction, these habitats reverted to more dense and uniform formations. Megafaunal extinction also led to changes in fire regimes and increased fire frequency due to accumulation of uncropped plant material, but there is a great deal of variation in post-extinction changes in fire. Plant communities that once interacted with extinct large herbivores still contain many species with obsolete defences against browsing and non-functional adaptations for seed dispersal. Such plants may be in decline, and, as a result, many plant communities may be in various stages of a process of relaxation from megafauna-conditioned to megafauna-naive states. Understanding the past role of giant herbivores provides fundamental insight into the history, dynamics and conservation of contemporary plant communities. PMID:19324773

Model for macroevolutionary dynamics.

PubMed

Maruvka, Yosef E; Shnerb, Nadav M; Kessler, David A; Ricklefs, Robert E

2013-07-02

The highly skewed distribution of species among genera, although challenging to macroevolutionists, provides an opportunity to understand the dynamics of diversification, including species formation, extinction, and morphological evolution. Early models were based on either the work by Yule [Yule GU (1925) Philos Trans R Soc Lond B Biol Sci 213:21-87], which neglects extinction, or a simple birth-death (speciation-extinction) process. Here, we extend the more recent development of a generic, neutral speciation-extinction (of species)-origination (of genera; SEO) model for macroevolutionary dynamics of taxon diversification. Simulations show that deviations from the homogeneity assumptions in the model can be detected in species-per-genus distributions. The SEO model fits observed species-per-genus distributions well for class-to-kingdom-sized taxonomic groups. The model's predictions for the appearance times (the time of the first existing species) of the taxonomic groups also approximately match estimates based on molecular inference and fossil records. Unlike estimates based on analyses of phylogenetic reconstruction, fitted extinction rates for large clades are close to speciation rates, consistent with high rates of species turnover and the relatively slow change in diversity observed in the fossil record. Finally, the SEO model generally supports the consistency of generic boundaries based on morphological differences between species and provides a comparator for rates of lineage splitting and morphological evolution.

Stickleback fishes: Bridging the gap between population biology and paleobiology.

PubMed

Bell, M A

1988-12-01

Integration of evolutionary mechanisms and phylogeny requires study of phenotypes that change in the fossil record and continue to evolve in extant populations. Pelvic reduction in the three-spined stickle-back has evolved rapidly in a Miocene fossil assemblage and in numerous extant isolated lake populations throughout its distribution. Although pelvic reduction is caused by selection, expression of reduced pelvic phenotypes is constrained by development and other factors. However, lineages with pelvis reduction rapidly go extinct while lineages that retain the fully formed pelvic girdle tend to persist. Existence of pelvic reduction since the Miocene has depended on an equilibrium between divergence and extinction. The phylogenetic topology resulting from this process differs greatly from the conventional view of evolutionary history, and could only be recognized by analysis of both extant populations and fossil material. If this phylogenetic topology is common, it may help to account for the different perceptions that population biologists and paleobiologists have of evolutionary tempo. Copyright © 1988. Published by Elsevier Ltd.

Global attractors and extinction dynamics of cyclically competing species.

PubMed

Rulands, Steffen; Zielinski, Alejandro; Frey, Erwin

2013-05-01

Transitions to absorbing states are of fundamental importance in nonequilibrium physics as well as ecology. In ecology, absorbing states correspond to the extinction of species. We here study the spatial population dynamics of three cyclically interacting species. The interaction scheme comprises both direct competition between species as in the cyclic Lotka-Volterra model, and separated selection and reproduction processes as in the May-Leonard model. We show that the dynamic processes leading to the transient maintenance of biodiversity are closely linked to attractors of the nonlinear dynamics for the overall species' concentrations. The characteristics of these global attractors change qualitatively at certain threshold values of the mobility and depend on the relative strength of the different types of competition between species. They give information about the scaling of extinction times with the system size and thereby the stability of biodiversity. We define an effective free energy as the negative logarithm of the probability to find the system in a specific global state before reaching one of the absorbing states. The global attractors then correspond to minima of this effective energy landscape and determine the most probable values for the species' global concentrations. As in equilibrium thermodynamics, qualitative changes in the effective free energy landscape indicate and characterize the underlying nonequilibrium phase transitions. We provide the complete phase diagrams for the population dynamics and give a comprehensive analysis of the spatio-temporal dynamics and routes to extinction in the respective phases.

Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation.

PubMed

Cosentino, Bradley J; Phillips, Christopher A; Schooley, Robert L; Lowe, Winsor H; Douglas, Marlis R

2012-04-22

Theory predicts that founder effects have a primary role in determining metapopulation genetic structure. However, ecological factors that affect extinction-colonization dynamics may also create spatial variation in the strength of genetic drift and migration. We tested the hypothesis that ecological factors underlying extinction-colonization dynamics influenced the genetic structure of a tiger salamander (Ambystoma tigrinum) metapopulation. We used empirical data on metapopulation dynamics to make a priori predictions about the effects of population age and ecological factors on genetic diversity and divergence among 41 populations. Metapopulation dynamics of A. tigrinum depended on wetland area, connectivity and presence of predatory fish. We found that newly colonized populations were more genetically differentiated than established populations, suggesting that founder effects influenced genetic structure. However, ecological drivers of metapopulation dynamics were more important than age in predicting genetic structure. Consistent with demographic predictions from metapopulation theory, genetic diversity and divergence depended on wetland area and connectivity. Divergence was greatest in small, isolated wetlands where genetic diversity was low. Our results show that ecological factors underlying metapopulation dynamics can be key determinants of spatial genetic structure, and that habitat area and isolation may mediate the contributions of drift and migration to divergence and evolution in local populations.

Quantitative traits and diversification.

PubMed

FitzJohn, Richard G

2010-12-01

Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.

Neural and Cellular Mechanisms of Fear and Extinction Memory Formation

PubMed Central

Orsini, Caitlin A.; Maren, Stephen

2012-01-01

Over the course of natural history, countless animal species have evolved adaptive behavioral systems to cope with dangerous situations and promote survival. Emotional memories are central to these defense systems because they are rapidly acquired and prepare organisms for future threat. Unfortunately, the persistence and intrusion of memories of fearful experiences are quite common and can lead to pathogenic conditions, such as anxiety and phobias. Over the course of the last thirty years, neuroscientists and psychologists alike have attempted to understand the mechanisms by which the brain encodes and maintains these aversive memories. Of equal interest, though, is the neurobiology of extinction memory formation as this may shape current therapeutic techniques. Here we review the extant literature on the neurobiology of fear and extinction memory formation, with a strong focus on the cellular and molecular mechanisms underlying these processes. PMID:22230704

Extinction threshold for spatial forest dynamics with height structure.

PubMed

Garcia-Domingo, Josep L; Saldaña, Joan

2011-05-07

We present a pair-approximation model for spatial forest dynamics defined on a regular lattice. The model assumes three possible states for a lattice site: empty (gap site), occupied by an immature tree, and occupied by a mature tree, and considers three nonlinearities in the dynamics associated to the processes of light interference, gap expansion, and recruitment. We obtain an expression of the basic reproduction number R(0) which, in contrast to the one obtained under the mean-field approach, uses information about the spatial arrangement of individuals close to extinction. Moreover, we analyze the corresponding survival-extinction transition of the forest and the spatial correlations among gaps, immature and mature trees close to this critical point. Predictions of the pair-approximation model are compared with those of a cellular automaton. Copyright © 2011 Elsevier Ltd. All rights reserved.

Extinction risk and eco-evolutionary dynamics in a variable environment with increasing frequency of extreme events.

PubMed

Vincenzi, Simone

2014-08-06

One of the most dramatic consequences of climate change will be the intensification and increased frequency of extreme events. I used numerical simulations to understand and predict the consequences of directional trend (i.e. mean state) and increased variability of a climate variable (e.g. temperature), increased probability of occurrence of point extreme events (e.g. floods), selection pressure and effect size of mutations on a quantitative trait determining individual fitness, as well as the their effects on the population and genetic dynamics of a population of moderate size. The interaction among climate trend, variability and probability of point extremes had a minor effect on risk of extinction, time to extinction and distribution of the trait after accounting for their independent effects. The survival chances of a population strongly and linearly decreased with increasing strength of selection, as well as with increasing climate trend and variability. Mutation amplitude had no effects on extinction risk, time to extinction or genetic adaptation to the new climate. Climate trend and strength of selection largely determined the shift of the mean phenotype in the population. The extinction or persistence of the populations in an 'extinction window' of 10 years was well predicted by a simple model including mean population size and mean genetic variance over a 10-year time frame preceding the 'extinction window', although genetic variance had a smaller role than population size in predicting contemporary risk of extinction. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Estimating rates of local extinction and colonization in colonial species and an extension to the metapopulation and community levels

USGS Publications Warehouse

Barbraud, C.; Nichols, J.D.; Hines, J.E.; Hafner, H.

2003-01-01

Coloniality has mainly been studied from an evolutionary perspective, but relatively few studies have developed methods for modelling colony dynamics. Changes in number of colonies over time provide a useful tool for predicting and evaluating the responses of colonial species to management and to environmental disturbance. Probabilistic Markov process models have been recently used to estimate colony site dynamics using presence-absence data when all colonies are detected in sampling efforts. Here, we define and develop two general approaches for the modelling and analysis of colony dynamics for sampling situations in which all colonies are, and are not, detected. For both approaches, we develop a general probabilistic model for the data and then constrain model parameters based on various hypotheses about colony dynamics. We use Akaike's Information Criterion (AIC) to assess the adequacy of the constrained models. The models are parameterised with conditional probabilities of local colony site extinction and colonization. Presence-absence data arising from Pollock's robust capture-recapture design provide the basis for obtaining unbiased estimates of extinction, colonization, and detection probabilities when not all colonies are detected. This second approach should be particularly useful in situations where detection probabilities are heterogeneous among colony sites. The general methodology is illustrated using presence-absence data on two species of herons (Purple Heron, Ardea purpurea and Grey Heron, Ardea cinerea). Estimates of the extinction and colonization rates showed interspecific differences and strong temporal and spatial variations. We were also able to test specific predictions about colony dynamics based on ideas about habitat change and metapopulation dynamics. We recommend estimators based on probabilistic modelling for future work on colony dynamics. We also believe that this methodological framework has wide application to problems in animal ecology concerning metapopulation and community dynamics.

CATS Version 2 Aerosol Feature Detection and Applications for Data Assimilation

NASA Technical Reports Server (NTRS)

Nowottnick, Ed; Yorks, John; McGill, Matt; Scott, Stan; Palm, Stephen; Hlavka, Dennis; Hart, William; Selmer, Patrick; Kupchock, Andrew; Pauly, Rebecca

2017-01-01

Using GEOS-5, we are developing a 1D ENS approach for assimilating CATS near real time observations of total attenuated backscatter at 1064 nm: a) After performing a 1-ENS assimilation of a cloud-free profile, the GEOS-5 analysis closely followed observed total attenuated backscatter. b) Vertical localization length scales were varied for the well-mixed PBL and the free troposphere After assimilating a cloud free segment of a CATS granule, the fine detail of a dust event was obtained in the GEOS-5 analysis for both total attenuated backscatter and extinction. Future Work: a) Explore horizontal localization and test within a cloudy aerosol layer. b) Address noisy analysis increments in the free troposphere where both CATS and GEOS-5 aerosol loadings are low. c) Develop a technique to screen CATS ground return from profiles. d) "Dynamic" lidar ratio that will evolve in conjunction with simulated aerosol mixtures.

No Love Lost Between Viruses and Interferons.

PubMed

Fensterl, Volker; Chattopadhyay, Saurabh; Sen, Ganes C

2015-11-01

The interferon system protects mammals against virus infections. There are several types of interferons, which are characterized by their ability to inhibit virus replication and resultant pathogenesis by triggering both innate and cell-mediated immune responses. Virus infection is sensed by a variety of cellular pattern-recognition receptors and triggers the synthesis of interferons, which are secreted by the infected cells. In uninfected cells, cell surface receptors recognize the secreted interferons and activate intracellular signaling pathways that induce the expression of interferon-stimulated genes; the proteins encoded by these genes inhibit different stages of virus replication. To avoid extinction, almost all viruses have evolved mechanisms to defend themselves against the interferon system. Consequently, a dynamic equilibrium of survival is established between the virus and its host, an equilibrium that can be shifted to the host's favor by the use of exogenous interferon as a therapeutic antiviral agent.

A resource-based game theoretical approach for the paradox of the plankton.

PubMed

Huang, Weini; de Araujo Campos, Paulo Roberto; Moraes de Oliveira, Viviane; Fagundes Ferrreira, Fernando

2016-01-01

The maintenance of species diversity is a central focus in ecology. It is not rare to observe more species than the number of limiting resources, especially in plankton communities. However, such high species diversity is hard to achieve in theory under the competitive exclusion principles, known as the plankton paradox. Previous studies often focus on the coexistence of predefined species and ignore the fact that species can evolve. We model multi-resource competitions using evolutionary games, where the number of species fluctuates under extinction and the appearance of new species. The interspecific and intraspecific competitions are captured by a dynamical payoff matrix, which has a size of the number of species. The competition strength (payoff entries) is obtained from comparing the capability of species in consuming resources, which can change over time. This allows for the robust coexistence of a large number of species, providing a possible solution to the plankton paradox.

A resource-based game theoretical approach for the paradox of the plankton

PubMed Central

de Araujo Campos, Paulo Roberto; Moraes de Oliveira, Viviane

2016-01-01

The maintenance of species diversity is a central focus in ecology. It is not rare to observe more species than the number of limiting resources, especially in plankton communities. However, such high species diversity is hard to achieve in theory under the competitive exclusion principles, known as the plankton paradox. Previous studies often focus on the coexistence of predefined species and ignore the fact that species can evolve. We model multi-resource competitions using evolutionary games, where the number of species fluctuates under extinction and the appearance of new species. The interspecific and intraspecific competitions are captured by a dynamical payoff matrix, which has a size of the number of species. The competition strength (payoff entries) is obtained from comparing the capability of species in consuming resources, which can change over time. This allows for the robust coexistence of a large number of species, providing a possible solution to the plankton paradox. PMID:27602293

Sexual selection affects local extinction and turnover in bird communities

USGS Publications Warehouse

Doherty, P.F.; Sorci, G.; Royle, J. Andrew; Hines, J.E.; Nichols, J.D.; Boulinier, T.

2003-01-01

Predicting extinction risks has become a central goal for conservation and evolutionary biologists interested in population and community dynamics. Several factors have been put forward to explain risks of extinction, including ecological and life history characteristics of individuals. For instance, factors that affect the balance between natality and mortality can have profound effects on population persistence. Sexual selection has been identified as one such factor. Populations under strong sexual selection experience a number of costs ranging from increased predation and parasitism to enhanced sensitivity to environmental and demographic stochasticity. These findings have led to the prediction that local extinction rates should be higher for species/populations with intense sexual selection. We tested this prediction by analyzing the dynamics of natural bird communities at a continental scale over a period of 21 years (1975-1996), using relevant statistical tools. In agreement with the theoretical prediction, we found that sexual selection increased risks of local extinction (dichromatic birds had on average a 23% higher local extinction rate than monochromatic species). However, despite higher local extinction probabilities, the number of dichromatic species did not decrease over the period considered in this study. This pattern was caused by higher local turnover rates of dichromatic species, resulting in relatively stable communities for both groups of species. Our results suggest that these communities function as metacommunities, with frequent local extinctions followed by colonization. Anthropogenic factors impeding dispersal might therefore have a significant impact on the global persistence of sexually selected species.

Is extinction forever?

PubMed Central

Bridge, Eli S.; Crawford, Priscilla H. C.; Hough, Daniel J.; Kelly, Jeffrey F.; Patten, Michael A.

2015-01-01

Mistrust of science has seeped into public perception of the most fundamental aspect of conservation—extinction. The term ought to be straightforward, and yet, there is a disconnect between scientific discussion and public views. This is not a mere semantic issue, rather one of communication. Within a population dynamics context, we say that a species went locally extinct, later to document its return. Conveying our findings matters, for when we use local extinction, an essentially nonsensical phrase, rather than extirpation, which is what is meant, then we contribute to, if not create outright, a problem for public understanding of conservation, particularly as local extinction is often shortened to extinction in media sources. The public that receives the message of our research void of context and modifiers comes away with the idea that extinction is not forever or, worse for conservation as a whole, that an extinction crisis has been invented. PMID:25711479

Dynamical scattering in coherent hard x-ray nanobeam Bragg diffraction

NASA Astrophysics Data System (ADS)

Pateras, A.; Park, J.; Ahn, Y.; Tilka, J. A.; Holt, M. V.; Kim, H.; Mawst, L. J.; Evans, P. G.

2018-06-01

Unique intensity features arising from dynamical diffraction arise in coherent x-ray nanobeam diffraction patterns of crystals having thicknesses larger than the x-ray extinction depth or exhibiting combinations of nanoscale and mesoscale features. We demonstrate that dynamical scattering effects can be accurately predicted using an optical model combined with the Darwin theory of dynamical x-ray diffraction. The model includes the highly divergent coherent x-ray nanobeams produced by Fresnel zone plate focusing optics and accounts for primary extinction, multiple scattering, and absorption. The simulation accurately reproduces the dynamical scattering features of experimental diffraction patterns acquired from a GaAs/AlGaAs epitaxial heterostructure on a GaAs (001) substrate.

When and where to move: Dynamic occupancy models explain the range dynamics of a food nomadic bird under climate and land cover change.

PubMed

Kalle, Riddhika; Ramesh, Tharmalingam; Downs, Colleen T

2018-01-01

Globally, long-term research is critical to monitor the responses of tropical species to climate and land cover change at the range scale. Citizen science surveys can reveal the long-term persistence of poorly known nomadic tropical birds occupying fragmented forest patches. We applied dynamic occupancy models to 13 years (2002-2014) of citizen science-driven presence/absence data on Cape parrot (Poicephalus robustus), a food nomadic bird endemic to South Africa. We modeled its underlying range dynamics as a function of resource distribution, and change in climate and land cover through the estimation of colonization and extinction patterns. The range occupancy of Cape parrot changed little over time (ψ = 0.75-0.83) because extinction was balanced by recolonization. Yet, there was considerable regional variability in occupancy and detection probability increased over the years. Colonizations increased with warmer temperature and area of orchards, thus explaining their range shifts southeastwards in recent years. Although colonizations were higher in the presence of nests and yellowwood trees (Afrocarpus and Podocarpus spp.), the extinctions in small forest patches (≤227 ha) and during low precipitation (≤41 mm) are attributed to resource constraints and unsuitable climatic conditions. Loss of indigenous forest cover and artificial lake/water bodies increased extinction probabilities of Cape parrot. The land use matrix (fruit farms, gardens, and cultivations) surrounding forest patches provides alternative food sources, thereby facilitating spatiotemporal colonization and extinction in the human-modified matrix. Our models show that Cape parrots are vulnerable to extreme climatic conditions such as drought which is predicted to increase under climate change. Therefore, management of optimum sized high-quality forest patches is essential for long-term survival of Cape parrot populations. Our novel application of dynamic occupancy models to long-term citizen science monitoring data unfolds the complex relationships between the environmental dynamics and range fluctuations of this food nomadic species. © 2017 John Wiley & Sons Ltd.

Neighborhood and habitat effects on vital rates: expansion of the Barred Owl in the Oregon Coast Ranges

USGS Publications Warehouse

Yackulic, Charles B.; Reid, Janice; Davis, Raymond; Hines, James E.; Nichols, James D.; Forsman, Eric

2012-01-01

In this paper, we modify dynamic occupancy models developed for detection-nondetection data to allow for the dependence of local vital rates on neighborhood occupancy, where neighborhood is defined very flexibly. Such dependence of occupancy dynamics on the status of a relevant neighborhood is pervasive, yet frequently ignored. Our framework permits joint inference about the importance of neighborhood effects and habitat covariates in determining colonization and extinction rates. Our specific motivation is the recent expansion of the Barred Owl (Strix varia) in western Oregon, USA, over the period 1990-2010. Because the focal period was one of dramatic range expansion and local population increase, the use of models that incorporate regional occupancy (sources of colonists) as determinants of dynamic rate parameters is especially appropriate. We began our analysis of 21 years of Barred Owl presence/nondetection data in the Tyee Density Study Area (TDSA) by testing a suite of six models that varied only in the covariates included in the modeling of detection probability. We then tested whether models that used regional occupancy as a covariate for colonization and extinction outperformed models with constant or year-specific colonization or extinction rates. Finally we tested whether habitat covariates improved the AIC of our models, focusing on which habitat covariates performed best, and whether the signs of habitat effects are consistent with a priori hypotheses. We conclude that all covariates used to model detection probability lead to improved AIC, that regional occupancy influences colonization and extinction rates, and that habitat plays an important role in determining extinction and colonization rates. As occupancy increases from low levels toward equilibrium, colonization increases and extinction decreases, presumably because there are more and more dispersing juveniles. While both rates are affected, colonization increases more than extinction decreases. Colonization is higher and extinction is lower in survey polygons with more riparian forest. The effects of riparian forest on extinction rates are greater than on colonization rates. Model results have implications for management of the invading Barred Owl, both through habitat alteration and removal.

Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

USGS Publications Warehouse

Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

2016-01-01

Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

Jurassic Park Insects

ERIC Educational Resources Information Center

Graff, Robert

2009-01-01

This lesson begins with a discussion on prehistoric times and how most life forms have either become extinct or have evolved into something people see in the environment today. Most of the conversation revolves around dinosaurs or animals on the endangered species list, such as the panda or polar bear. The author directed the conversation to…

Gradual Dinosaur Extinction and Simultaneous Ungulate Radiation in the Hell Creek Formation

NASA Astrophysics Data System (ADS)

Sloan, Robert E.; Rigby, J. Keith; van Valen, Leigh M.; Gabriel, Diane

1986-05-01

Dinosaur extinction in Montana, Alberta, and Wyoming was a gradual process that began 7 million years before the end of the Cretaceous and accelerated rapidly in the final 0.3 million years of the Cretaceous, during the interval of apparent competition from rapidly evolving immigrating ungulates. This interval involves rapid reduction in both diversity and population density of dinosaurs. The last dinosaurs known are from a channel that contains teeth of Mantuan mammals, seven species of dinosaurs, and Paleocene pollen. The top of this channel is 1.3 meters above the likely position of the iridium anomaly, the Cretaceous/Tertiary boundary.

Confounding environmental colour and distribution shape leads to underestimation of population extinction risk.

PubMed

Fowler, Mike S; Ruokolainen, Lasse

2013-01-01

The colour of environmental variability influences the size of population fluctuations when filtered through density dependent dynamics, driving extinction risk through dynamical resonance. Slow fluctuations (low frequencies) dominate in red environments, rapid fluctuations (high frequencies) in blue environments and white environments are purely random (no frequencies dominate). Two methods are commonly employed to generate the coloured spatial and/or temporal stochastic (environmental) series used in combination with population (dynamical feedback) models: autoregressive [AR(1)] and sinusoidal (1/f) models. We show that changing environmental colour from white to red with 1/f models, and from white to red or blue with AR(1) models, generates coloured environmental series that are not normally distributed at finite time-scales, potentially confounding comparison with normally distributed white noise models. Increasing variability of sample Skewness and Kurtosis and decreasing mean Kurtosis of these series alter the frequency distribution shape of the realised values of the coloured stochastic processes. These changes in distribution shape alter patterns in the probability of single and series of extreme conditions. We show that the reduced extinction risk for undercompensating (slow growing) populations in red environments previously predicted with traditional 1/f methods is an artefact of changes in the distribution shapes of the environmental series. This is demonstrated by comparison with coloured series controlled to be normally distributed using spectral mimicry. Changes in the distribution shape that arise using traditional methods lead to underestimation of extinction risk in normally distributed, red 1/f environments. AR(1) methods also underestimate extinction risks in traditionally generated red environments. This work synthesises previous results and provides further insight into the processes driving extinction risk in model populations. We must let the characteristics of known natural environmental covariates (e.g., colour and distribution shape) guide us in our choice of how to best model the impact of coloured environmental variation on population dynamics.

Dinosaurs in decline tens of millions of years before their final extinction

PubMed Central

Sakamoto, Manabu; Benton, Michael J.; Venditti, Chris

2016-01-01

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous–Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event. PMID:27092007

Dinosaurs in decline tens of millions of years before their final extinction.

PubMed

Sakamoto, Manabu; Benton, Michael J; Venditti, Chris

2016-05-03

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous-Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event.

Dinosaurs in decline tens of millions of years before their final extinction

NASA Astrophysics Data System (ADS)

Sakamoto, Manabu; Benton, Michael J.

2016-05-01

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous-Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event.

Pattern does not equal process: what does patch occupancy really tell us about metapopulation dynamics?

PubMed

Clinchy, Michael; Haydon, Daniel T; Smith, Andrew T

2002-04-01

Patch occupancy surveys are commonly used to parameterize metapopulation models. If isolation predicts patch occupancy, this is generally attributed to a balance between distance-dependent recolonization and spatially independent extinctions. We investigated whether similar patterns could also be generated by a process of spatially correlated extinctions following a unique colonization event (analogous to nonequilibrium processes in island biogeography). We simulated effects of spatially correlated extinctions on patterns of patch occupancy among pikas (Ochotona princeps) at Bodie, California, using randomly located extinction disks to represent the likely effects of predation. Our simulations produced similar patterns to those cited as evidence of balanced metapopulation dynamics. Simulations using a variety of disk sizes and patch configurations confirmed that our results are potentially applicable to a broad range of species and sites. Analyses of the observed patterns of patch occupancy at Bodie revealed little evidence of rescue effects and strong evidence that most recolonizations are ephemeral in nature. Persistence will be overestimated if static or declining patterns of patch occupancy are mistakenly attributed to dynamically stable metapopulation processes. Consequently, simple patch occupancy surveys should not be considered as substitutes for detailed experimental tests of hypothesized population processes, particularly when conservation concerns are involved.

Diversity Driven Coexistence: Collective Stability in the Cyclic Competition of Three Species

NASA Astrophysics Data System (ADS)

Bassler, Kevin E.; Frey, Erwin; Zia, R. K. P.

2015-03-01

The basic physics of collective behavior are often difficult to quantify and understand, particularly when the system is driven out of equilibrium. Many complex systems are usefully described as complex networks, consisting of nodes and links. The nodes specify individual components of the system and the links describe their interactions. When both nodes and links change dynamically, or `co-evolve', as happens in many realistic systems, complex mathematical structures are encountered, posing challenges to our understanding. In this context, we introduce a minimal system of node and link degrees of freedom, co-evolving with stochastic rules. Specifically, we show that diversity of social temperament (intro- or extroversion) can produce collective stable coexistence when three species compete cyclically. It is well-known that when only extroverts exist in a stochastic rock-paper-scissors game, or in a conserved predator-prey, Lotka-Volterra system, extinction occurs at times of O(N), where N is the number of nodes. We find that when both introverts and extroverts exist, where introverts sever social interactions and extroverts create them, collective coexistence prevails in long-living, quasi-stationary states. Work supported by the NSF through Grants DMR-1206839 (KEB) and DMR-1244666 (RKPZ), and by the AFOSR and DARPA through Grant FA9550-12-1-0405 (KEB).

Biodiversity and ecosystem functioning in evolving food webs.

PubMed

Allhoff, K T; Drossel, B

2016-05-19

We use computer simulations in order to study the interplay between biodiversity and ecosystem functioning (BEF) during both the formation and the ongoing evolution of large food webs. A species in our model is characterized by its own body mass, its preferred prey body mass and the width of its potential prey body mass spectrum. On an ecological time scale, population dynamics determines which species are viable and which ones go extinct. On an evolutionary time scale, new species emerge as modifications of existing ones. The network structure thus emerges and evolves in a self-organized manner. We analyse the relation between functional diversity and five community level measures of ecosystem functioning. These are the metabolic loss of the predator community, the total biomasses of the basal and the predator community, and the consumption rates on the basal community and within the predator community. Clear BEF relations are observed during the initial build-up of the networks, or when parameters are varied, causing bottom-up or top-down effects. However, ecosystem functioning measures fluctuate only very little during long-term evolution under constant environmental conditions, despite changes in functional diversity. This result supports the hypothesis that trophic cascades are weaker in more complex food webs. © 2016 The Author(s).

Commentary on Holmes et al. (2007): resolving the debate on when extinction risk is predictable.

PubMed

Ellner, Stephen P; Holmes, Elizabeth E

2008-08-01

We reconcile the findings of Holmes et al. (Ecology Letters, 10, 2007, 1182) that 95% confidence intervals for quasi-extinction risk were narrow for many vertebrates of conservation concern, with previous theory predicting wide confidence intervals. We extend previous theory, concerning the precision of quasi-extinction estimates as a function of population dynamic parameters, prediction intervals and quasi-extinction thresholds, and provide an approximation that specifies the prediction interval and threshold combinations where quasi-extinction estimates are precise (vs. imprecise). This allows PVA practitioners to define the prediction interval and threshold regions of safety (low risk with high confidence), danger (high risk with high confidence), and uncertainty.

Spatially Synchronous Extinction of Species under External Forcing

NASA Astrophysics Data System (ADS)

Amritkar, R. E.; Rangarajan, Govindan

2006-06-01

More than 99% of the species that ever existed on the surface of the Earth are now extinct and their extinction on a global scale has been a puzzle. One may think that a species under an external threat may survive in some isolated locations leading to the revival of the species. Using a general model we show that, under a common external forcing, the species with a quadratic saturation term first undergoes spatial synchronization and then extinction. The effect can be observed even when the external forcing acts only on some locations provided the dynamics contains a synchronizing term. Absence of the quadratic saturation term can help the species to avoid extinction.

Quantifying the severity of hurricanes on extinction probabilities of a primate population: Insights into "Island" extirpations.

PubMed

Ameca y Juárez, Eric I; Ellis, Edward A; Rodríguez-Luna, Ernesto

2015-07-01

Long-term studies quantifying impacts of hurricane activity on growth and trajectory of primate populations are rare. Using a 14-year monitored population of Alouatta palliata mexicana as a study system, we developed a modeling framework to assess the relative contribution of hurricane disturbance and two types of human impacts, habitat loss, and hunting, on quasi-extinction risk. We found that the scenario with the highest level of disturbance generated a 21% increase in quasi-extinction risk by 40 years compared to scenarios of intermediate disturbance, and around 67% increase relative to that found in low disturbance scenarios. We also found that the probability of reaching quasi-extinction due to human disturbance alone was below 1% by 40 years, although such scenarios reduced population size by 70%, whereas the risk of quasi-extinction ranged between 3% and 65% for different scenarios of hurricane severity alone, in absence of human impacts. Our analysis moreover found that the quasi-extinction risk driven by hunting and hurricane disturbance was significantly lower than the quasi-extinction risk posed by human-driven habitat loss and hurricane disturbance. These models suggest that hurricane disturbance has the potential to exceed the risk posed by human impacts, and, in particular, to substantially increase the speed of the extinction vortex driven by habitat loss relative to that driven by hunting. Early mitigation of habitat loss constituted the best method for reducing quasi-extinction risk: the earlier habitat loss is halted, the less vulnerable the population becomes to hurricane disturbance. By using a well-studied population of A. p. mexicana, we help understand the demographic impacts that extreme environmental disturbance can trigger on isolated populations of taxa already endangered in other systems where long-term demographic data are not available. For those experiencing heavy anthropogenic pressure and lacking sufficiently evolved coping strategies against unpredictable environmental disturbance, the risk of population extinction can be exacerbated. © 2015 Wiley Periodicals, Inc.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

Colonization and extinction in dynamic habitats: an occupancy approach for a Great Plains stream fish assemblage.

PubMed

Falke, Jeffrey A; Bailey, Larissa L; Fausch, Kurt D; Bestgen, Kevin R

2012-04-01

Despite the importance of habitat in determining species distribution and persistence, habitat dynamics are rarely modeled in studies of metapopulations. We used an integrated habitat-occupancy model to simultaneously quantify habitat change, site fidelity, and local colonization and extinction rates for larvae of a suite of Great Plains stream fishes in the Arikaree River, eastern Colorado, USA, across three years. Sites were located along a gradient of flow intermittency and groundwater connectivity. Hydrology varied across years: the first and third being relatively wet and the second dry. Despite hydrologic variation, our results indicated that site suitability was random from one year to the next. Occupancy probabilities were also independent of previous habitat and occupancy state for most species, indicating little site fidelity. Climate and groundwater connectivity were important drivers of local extinction and colonization, but the importance of groundwater differed between periods. Across species, site extinction probabilities were highest during the transition from wet to dry conditions (range: 0.52-0.98), and the effect of groundwater was apparent with higher extinction probabilities for sites not fed by groundwater. Colonization probabilities during this period were relatively low for both previously dry sites (range: 0.02-0.38) and previously wet sites (range: 0.02-0.43). In contrast, no sites dried or remained dry during the transition from dry to wet conditions, yielding lower but still substantial extinction probabilities (range: 0.16-0.63) and higher colonization probabilities (range: 0.06-0.86), with little difference among sites with and without groundwater. This approach of jointly modeling both habitat change and species occupancy will likely be useful to incorporate effects of dynamic habitat on metapopulation processes and to better inform appropriate conservation actions.

Exposing extinction risk analysis to pathogens: Is disease just another form of density dependence?

USGS Publications Warehouse

Gerber, L.R.; McCallum, H.; Lafferty, K.D.; Sabo, J.L.; Dobson, A.

2005-01-01

In the United States and several other countries, the development of population viability analyses (PVA) is a legal requirement of any species survival plan developed for threatened and endangered species. Despite the importance of pathogens in natural populations, little attention has been given to host-pathogen dynamics in PVA. To study the effect of infectious pathogens on extinction risk estimates generated from PVA, we review and synthesize the relevance of host-pathogen dynamics in analyses of extinction risk. We then develop a stochastic, density-dependent host-parasite model to investigate the effects of disease on the persistence of endangered populations. We show that this model converges on a Ricker model of density dependence under a suite of limiting assumptions, including a high probability that epidemics will arrive and occur. Using this modeling framework, we then quantify: (1) dynamic differences between time series generated by disease and Ricker processes with the same parameters; (2) observed probabilities of quasi-extinction for populations exposed to disease or self-limitation; and (3) bias in probabilities of quasi-extinction estimated by density-independent PVAs when populations experience either form of density dependence. Our results suggest two generalities about the relationships among disease, PVA, and the management of endangered species. First, disease more strongly increases variability in host abundance and, thus, the probability of quasi-extinction, than does self-limitation. This result stems from the fact that the effects and the probability of occurrence of disease are both density dependent. Second, estimates of quasi-extinction are more often overly optimistic for populations experiencing disease than for those subject to self-limitation. Thus, although the results of density-independent PVAs may be relatively robust to some particular assumptions about density dependence, they are less robust when endangered populations are known to be susceptible to disease. If potential management actions involve manipulating pathogens, then it may be useful to model disease explicitly. ?? 2005 by the Ecological Society of America.

My Pencils Have Names

ERIC Educational Resources Information Center

Block, Phillip

2011-01-01

As personal computers have evolved steadily into handhelds and teachers continue the march toward lining the walls of the classroom with flat screen work stations, many assume that the old-timey "number 2" lead yellow pencil is probably on the high road to extinction. Yet most classrooms still flow with them like miniature telephone poles fresh…

Extinction Dynamics and Control in Adaptive Networks

NASA Astrophysics Data System (ADS)

Schwartz, Ira; Shaw, Leah; Hindes, Jason

Disease control is of paramount importance in public health. Moreover, models of disease spread are an important component in implementing effective vaccination and treatment campaigns. However, human behavior in response to an outbreak has only recently been included in epidemic models on networks. Here we develop the mathematical machinery to describe the dynamics of extinction in finite populations that include human adaptive behavior. The formalism enables us to compute the optimal, fluctuation-induced path to extinction, and predict the average extinction time in adaptive networks as a function of the adaptation rate. We find that both observables have several unique scalings depending on the relative speed of infection and adaptivity. Finally, we discuss how the theory can be used to design optimal control programs in general networks, by coupling the effective force of noise with treatment and human behavior. Research supported by U.S. Naval Research Laboratory funding (Grant No. N0001414WX00023) and the Office of Naval Research (Grant No. N0001414WX20610).

Pleistocene megafaunal interaction networks became more vulnerable after human arrival.

PubMed

Pires, Mathias M; Koch, Paul L; Fariña, Richard A; de Aguiar, Marcus A M; dos Reis, Sérgio F; Guimarães, Paulo R

2015-09-07

The end of the Pleistocene was marked by the extinction of almost all large land mammals worldwide except in Africa. Although the debate on Pleistocene extinctions has focused on the roles of climate change and humans, the impact of perturbations depends on properties of ecological communities, such as species composition and the organization of ecological interactions. Here, we combined palaeoecological and ecological data, food-web models and community stability analysis to investigate if differences between Pleistocene and modern mammalian assemblages help us understand why the megafauna died out in the Americas while persisting in Africa. We show Pleistocene and modern assemblages share similar network topology, but differences in richness and body size distributions made Pleistocene communities significantly more vulnerable to the effects of human arrival. The structural changes promoted by humans in Pleistocene networks would have increased the likelihood of unstable dynamics, which may favour extinction cascades in communities facing extrinsic perturbations. Our findings suggest that the basic aspects of the organization of ecological communities may have played an important role in major extinction events in the past. Knowledge of community-level properties and their consequences to dynamics may be critical to understand past and future extinctions. © 2015 The Author(s).

Pleistocene megafaunal interaction networks became more vulnerable after human arrival

PubMed Central

Pires, Mathias M.; Koch, Paul L.; Fariña, Richard A.; de Aguiar, Marcus A. M.; dos Reis, Sérgio F.; Guimarães, Paulo R.

2015-01-01

The end of the Pleistocene was marked by the extinction of almost all large land mammals worldwide except in Africa. Although the debate on Pleistocene extinctions has focused on the roles of climate change and humans, the impact of perturbations depends on properties of ecological communities, such as species composition and the organization of ecological interactions. Here, we combined palaeoecological and ecological data, food-web models and community stability analysis to investigate if differences between Pleistocene and modern mammalian assemblages help us understand why the megafauna died out in the Americas while persisting in Africa. We show Pleistocene and modern assemblages share similar network topology, but differences in richness and body size distributions made Pleistocene communities significantly more vulnerable to the effects of human arrival. The structural changes promoted by humans in Pleistocene networks would have increased the likelihood of unstable dynamics, which may favour extinction cascades in communities facing extrinsic perturbations. Our findings suggest that the basic aspects of the organization of ecological communities may have played an important role in major extinction events in the past. Knowledge of community-level properties and their consequences to dynamics may be critical to understand past and future extinctions. PMID:26336175

Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series

PubMed Central

Ferguson, Jake M; Ponciano, José M

2014-01-01

Predicting population extinction risk is a fundamental application of ecological theory to the practice of conservation biology. Here, we compared the prediction performance of a wide array of stochastic, population dynamics models against direct observations of the extinction process from an extensive experimental data set. By varying a series of biological and statistical assumptions in the proposed models, we were able to identify the assumptions that affected predictions about population extinction. We also show how certain autocorrelation structures can emerge due to interspecific interactions, and that accounting for the stochastic effect of these interactions can improve predictions of the extinction process. We conclude that it is possible to account for the stochastic effects of community interactions on extinction when using single-species time series. PMID:24304946

Extinction debt from climate change for frogs in the wet tropics

PubMed Central

Brook, Barry W.; Hoskin, Conrad J.; Pressey, Robert L.; VanDerWal, Jeremy; Williams, Stephen E.

2016-01-01

The effect of twenty-first-century climate change on biodiversity is commonly forecast based on modelled shifts in species ranges, linked to habitat suitability. These projections have been coupled with species–area relationships (SAR) to infer extinction rates indirectly as a result of the loss of climatically suitable areas and associated habitat. This approach does not model population dynamics explicitly, and so accepts that extinctions might occur after substantial (but unknown) delays—an extinction debt. Here we explicitly couple bioclimatic envelope models of climate and habitat suitability with generic life-history models for 24 species of frogs found in the Australian Wet Tropics (AWT). We show that (i) as many as four species of frogs face imminent extinction by 2080, due primarily to climate change; (ii) three frogs face delayed extinctions; and (iii) this extinction debt will take at least a century to be realized in full. Furthermore, we find congruence between forecast rates of extinction using SARs, and demographic models with an extinction lag of 120 years. We conclude that SAR approaches can provide useful advice to conservation on climate change impacts, provided there is a good understanding of the time lags over which delayed extinctions are likely to occur. PMID:27729484

Life History Correlates and Extinction Risk of Capital-Breeding Fishes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jager, Yetta; Vila-Gispert, Dr Anna; Rose, Kenneth A.

2008-03-01

We consider a distinction for fishes, often made for birds and reptiles, between capital-breeding and income-breeding species. Species that follow a capital-breeding strategy tend to evolve longer intervals between reproductive events and tend to have characteristics that we associate with higher extinction risk. To examine whether these ideas are relevant for fishes, we assembled life-history data for fish species, including an index of extinction risk, the interval between spawning events, the degree of parental care, and whether or not the species migrates to spawn. These data were used to evaluate two hypotheses: 1) fish species with a major accessory activitymore » to spawning (migration or parental care) spawn less often and 2) fish species that spawn less often are at greater risk of extinction. We tested these hypotheses by applying two alternative statistical methods that account for phylogenetic correlation in cross-taxon comparisons. The two methods predicted average intervals between spawning events 0.13 to 0.20 years longer for fishes with a major accessory activity. Both accessories, above-average parental care and spawning migration, were individually associated with longer average spawning intervals. We conclude that the capital-breeding paradigm is relevant for fishes. We also confirmed the second hypothesis, that species in higher IUCN extinction risk categories had longer average spawning intervals. Further research is needed to understand the relationship between extinction risk and spawning interval, within the broader context of life history traits and aquatic habitats.« less

The role of climate and vegetation on woolly mammoth extinction on St. Paul Island, Alaska and megafauna extinction in North America in the late Quaternary

NASA Astrophysics Data System (ADS)

Wang, Y.; Porter, W.; Miller, P. A.; Graham, R. W.; Williams, J. W.

2016-12-01

Estimate of megafauna behaviors dynamically under associated environmental factors is important to understand the mechanisms and causes of the late Quaternary megafaunal extinctions. On St. Paul Island, an isolated remnant of the Bering Land Bridge, a late-surviving population of woolly mammoth (Mammuthus primigenius) persisted until 5,600 cal BP, while 37 out of 54 megafauna species in the continent of North America, all herbivores, went extinct at the end of Pleistocene between 13,800 and 11,500 cal BP. Proposed natural drivers of the extinction events include abrupt temperature changes, food resource loss and freshwater shortage. Here we tested these three hypothesized mechanisms, using a physiological model (Niche Mapper) to estimate individual megafauna behaviors from the perspectives of metabolic rate, individual vegetation and freshwater requirement under simulated climates from Community Climate System Model version 3 (CCSM3), vegetation reconstructions based on dynamic LPJ-GUESS model and woolly mammoth and megafauna species trait data reconstructed based on mammal fossils. Preliminary simulations of woolly mammoth on St. Paul Island point to the importance of net vegetation primary productivity and freshwater availability as limits on the carrying capacity of St. Paul for mammoth populations, with a low carrying capacity in the middle Holocene making this population highly vulnerable to extinction. Results also indicate that the abrupt warming based around 14,000 cal BP in Bering land bridge on CCSM3 simulations causes woolly mammoth extinction, by driving metabolic rate high up beyond the active basic metabolic rate. Analysis suggests a positive relationship between temperature and metabolic rate, and woolly mammoth would go extinct when summer temperature is up to 12 °C or higher. However the temperature reconstructed based on regional proxies is relatively stable compared to CCSM3 simulations, and leads to stable metabolic rate of woolly mammoth and no extinction events. Proposed simulations of megafauna species in North America indicate the role of ice sheets in limiting habitats. This work helps resolve the drivers of extinction for a small island surviving woolly mammoth population and worldwide megafauna extinctions in the late Quaternary.

Stochastic hybrid delay population dynamics: well-posed models and extinction.

PubMed

Yuan, Chenggui; Mao, Xuerong; Lygeros, John

2009-01-01

Nonlinear differential equations have been used for decades for studying fluctuations in the populations of species, interactions of species with the environment, and competition and symbiosis between species. Over the years, the original non-linear models have been embellished with delay terms, stochastic terms and more recently discrete dynamics. In this paper, we investigate stochastic hybrid delay population dynamics (SHDPD), a very general class of population dynamics that comprises all of these phenomena. For this class of systems, we provide sufficient conditions to ensure that SHDPD have global positive, ultimately bounded solutions, a minimum requirement for a realistic, well-posed model. We then study the question of extinction and establish conditions under which an ecosystem modelled by SHDPD is doomed.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly

PubMed Central

Hanski, Ilkka A.

2011-01-01

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time. PMID:21788506

Rarity in mass extinctions and the future of ecosystems

NASA Astrophysics Data System (ADS)

Hull, Pincelli M.; Darroch, Simon A. F.; Erwin, Douglas H.

2015-12-01

The fossil record provides striking case studies of biodiversity loss and global ecosystem upheaval. Because of this, many studies have sought to assess the magnitude of the current biodiversity crisis relative to past crises—a task greatly complicated by the need to extrapolate extinction rates. Here we challenge this approach by showing that the rarity of previously abundant taxa may be more important than extinction in the cascade of events leading to global changes in the biosphere. Mass rarity may provide the most robust measure of our current biodiversity crisis relative to those past, and new insights into the dynamics of mass extinction.

Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series.

PubMed

Ferguson, Jake M; Ponciano, José M

2014-02-01

Predicting population extinction risk is a fundamental application of ecological theory to the practice of conservation biology. Here, we compared the prediction performance of a wide array of stochastic, population dynamics models against direct observations of the extinction process from an extensive experimental data set. By varying a series of biological and statistical assumptions in the proposed models, we were able to identify the assumptions that affected predictions about population extinction. We also show how certain autocorrelation structures can emerge due to interspecific interactions, and that accounting for the stochastic effect of these interactions can improve predictions of the extinction process. We conclude that it is possible to account for the stochastic effects of community interactions on extinction when using single-species time series. © 2013 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

Trophic network models explain instability of Early Triassic terrestrial communities

PubMed Central

Roopnarine, Peter D; Angielczyk, Kenneth D; Wang, Steve C; Hertog, Rachel

2007-01-01

Studies of the end-Permian mass extinction have emphasized potential abiotic causes and their direct biotic effects. Less attention has been devoted to secondary extinctions resulting from ecological crises and the effect of community structure on such extinctions. Here we use a trophic network model that combines topological and dynamic approaches to simulate disruptions of primary productivity in palaeocommunities. We apply the model to Permian and Triassic communities of the Karoo Basin, South Africa, and show that while Permian communities bear no evidence of being especially susceptible to extinction, Early Triassic communities appear to have been inherently less stable. Much of the instability results from the faster post-extinction diversification of amphibian guilds relative to amniotes. The resulting communities differed fundamentally in structure from their Permian predecessors. Additionally, our results imply that changing community structures over time may explain long-term trends like declining rates of Phanerozoic background extinction PMID:17609191

Late Maastrichtian pterosaurs from North Africa and mass extinction of Pterosauria at the Cretaceous-Paleogene boundary

PubMed Central

Martill, David M.; Andres, Brian

2018-01-01

Pterosaurs were the first vertebrates to evolve powered flight and the largest animals to ever take wing. The pterosaurs persisted for over 150 million years before disappearing at the end of the Cretaceous, but the patterns of and processes driving their extinction remain unclear. Only a single family, Azhdarchidae, is definitively known from the late Maastrichtian, suggesting a gradual decline in diversity in the Late Cretaceous, with the Cretaceous–Paleogene (K-Pg) extinction eliminating a few late-surviving species. However, this apparent pattern may simply reflect poor sampling of fossils. Here, we describe a diverse pterosaur assemblage from the late Maastrichtian of Morocco that includes not only Azhdarchidae but the youngest known Pteranodontidae and Nyctosauridae. With 3 families and at least 7 species present, the assemblage represents the most diverse known Late Cretaceous pterosaur assemblage and dramatically increases the diversity of Maastrichtian pterosaurs. At least 3 families—Pteranodontidae, Nyctosauridae, and Azhdarchidae—persisted into the late Maastrichtian. Late Maastrichtian pterosaurs show increased niche occupation relative to earlier, Santonian-Campanian faunas and successfully outcompeted birds at large sizes. These patterns suggest an abrupt mass extinction of pterosaurs at the K-Pg boundary. PMID:29534059

Dispersal, niche breadth and population extinction: colonization ratios predict range size in North American dragonflies.

PubMed

McCauley, Shannon J; Davis, Christopher J; Werner, Earl E; Robeson, Michael S

2014-07-01

Species' range sizes are shaped by fundamental differences in species' ecological and evolutionary characteristics, and understanding the mechanisms determining range size can shed light on the factors responsible for generating and structuring biological diversity. Moreover, because geographic range size is associated with a species' risk of extinction and their ability to respond to global changes in climate and land use, understanding these mechanisms has important conservation implications. Despite the hypotheses that dispersal behaviour is a strong determinant of species range areas, few data are available to directly compare the relationship between dispersal behaviour and range size. Here, we overcome this limitation by combining data from a multispecies dispersal experiment with additional species-level trait data that are commonly hypothesized to affect range size (e.g. niche breadth, local abundance and body size.). This enables us to examine the relationship between these species-level traits and range size across North America for fifteen dragonfly species. Ten models based on a priori predictions about the relationship between species traits and range size were evaluated and two models were identified as good predictors of species range size. These models indicated that only two species' level traits, dispersal behaviour and niche breadth were strongly related to range size. The evidence from these two models indicated that dragonfly species that disperse more often and further had larger North American ranges. Extinction and colonization dynamics are expected to be a key linkage between dispersal behaviour and range size in dragonflies. To evaluate how extinction and colonization dynamics among dragonflies were related to range size we used an independent data set of extinction and colonization rates for eleven dragonfly species and assessed the relationship between these populations rates and North American range areas for these species. We found a negative relationship between North American range size and species' extinction-to-colonization ratios. Our results indicate that metapopulation dynamics act to shape the extent of species' continental distributions. These population dynamics are likely to interact with dispersal behaviour, particularly at species range margins, to determine range limits and ultimately species range sizes. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Co-extinction in a host-parasite network: identifying key hosts for network stability.

PubMed

Dallas, Tad; Cornelius, Emily

2015-08-17

Parasites comprise a substantial portion of total biodiversity. Ultimately, this means that host extinction could result in many secondary extinctions of obligate parasites and potentially alter host-parasite network structure. Here, we examined a highly resolved fish-parasite network to determine key hosts responsible for maintaining parasite diversity and network structure (quantified here as nestedness and modularity). We evaluated four possible host extinction orders and compared the resulting co-extinction dynamics to random extinction simulations; including host removal based on estimated extinction risk, parasite species richness and host level contributions to nestedness and modularity. We found that all extinction orders, except the one based on realistic extinction risk, resulted in faster declines in parasite diversity and network structure relative to random biodiversity loss. Further, we determined species-level contributions to network structure were best predicted by parasite species richness and host family. Taken together, we demonstrate that a small proportion of hosts contribute substantially to network structure and that removal of these hosts results in rapid declines in parasite diversity and network structure. As network stability can potentially be inferred through measures of network structure, our findings may provide insight into species traits that confer stability.

Retrieval method of aerosol extinction coefficient profile by an integral lidar system and case study

NASA Astrophysics Data System (ADS)

Shan, Huihui; Zhang, Hui; Liu, Junjian; Wang, Shenhao; Ma, Xiaomin; Zhang, Lianqing; Liu, Dong; Xie, Chenbo; Tao, Zongming

2018-02-01

Aerosol extinction coefficient profile is an essential parameter for atmospheric radiation model. But it is difficult to get the full aerosol extinction profile from the ground to the tropopause especially in near ground precisely using backscattering lidar. A combined measurement of side-scattering, backscattering and Raman-scattering lidar is proposed to retrieve the aerosol extinction coefficient profile from the surface to the tropopause which covered a dynamic range of 5 orders. The side-scattering technique solves the dead zone and the overlap problem caused by the traditional lidar in the near range. Using the Raman-scattering the aerosol lidar ratio (extinction to backscatter ratio) can be obtained. The cases studies in this paper show the proposed method is reasonable and feasible.

Laplacian Estrada and normalized Laplacian Estrada indices of evolving graphs.

PubMed

Shang, Yilun

2015-01-01

Large-scale time-evolving networks have been generated by many natural and technological applications, posing challenges for computation and modeling. Thus, it is of theoretical and practical significance to probe mathematical tools tailored for evolving networks. In this paper, on top of the dynamic Estrada index, we study the dynamic Laplacian Estrada index and the dynamic normalized Laplacian Estrada index of evolving graphs. Using linear algebra techniques, we established general upper and lower bounds for these graph-spectrum-based invariants through a couple of intuitive graph-theoretic measures, including the number of vertices or edges. Synthetic random evolving small-world networks are employed to show the relevance of the proposed dynamic Estrada indices. It is found that neither the static snapshot graphs nor the aggregated graph can approximate the evolving graph itself, indicating the fundamental difference between the static and dynamic Estrada indices.

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions

PubMed Central

Zu, Jian; Wang, Jinliang; Huang, Gang

2016-01-01

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey’s trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator’s trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions. PMID:27685540

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions.

PubMed

Zu, Jian; Wang, Jinliang; Huang, Gang

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey's trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator's trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions.

Dietary Specialization during the Evolution of Western Eurasian Hominoids and the Extinction of European Great Apes

PubMed Central

DeMiguel, Daniel; Alba, David M.; Moyà-Solà, Salvador

2014-01-01

Given the central adaptive role of diet, paleodietary inference is essential for understanding the relationship between evolutionary and paleoenvironmental change. Here we rely on dental microwear analysis to investigate the role of dietary specialization in the diversification and extinction of Miocene hominoids from Western Eurasian between 14 and 7 Ma. New microwear results for five extinct taxa are analyzed together with previous data for other Western Eurasian genera. Except Pierolapithecus (that resembles hard-object feeders) and Oreopithecus (a soft-frugivore probably foraging opportunistically on other foods), most of the extinct taxa lack clear extant dietary analogues. They display some degee of sclerocarpy, which is most clearly expressed in Griphopithecus and Ouranopithecus (adapted to more open and arid environments), whereas Anoiapithecus, Dryopithecus and, especially, Hispanopithecus species apparently relied more strongly on soft-frugivory. Thus, contrasting with the prevailing sclerocarpic condition at the beginning of the Eurasian hominoid radiation, soft- and mixed-frugivory coexisted with hard-object feeding in the Late Miocene. Therefore, despite a climatic trend towards cooling and increased seasonality, a progressive dietary diversification would have occurred (probably due to competitive exclusion and increased environmental heterogeneity), although strict folivory did not evolve. Overall, our analyses support the view that the same dietary specializations that enabled Western Eurasian hominoids to face progressive climatic deterioration were the main factor ultimately leading to their extinction when more drastic paleoenvironmental changes took place. PMID:24848272

Extinction debt from climate change for frogs in the wet tropics.

PubMed

Fordham, Damien A; Brook, Barry W; Hoskin, Conrad J; Pressey, Robert L; VanDerWal, Jeremy; Williams, Stephen E

2016-10-01

The effect of twenty-first-century climate change on biodiversity is commonly forecast based on modelled shifts in species ranges, linked to habitat suitability. These projections have been coupled with species-area relationships (SAR) to infer extinction rates indirectly as a result of the loss of climatically suitable areas and associated habitat. This approach does not model population dynamics explicitly, and so accepts that extinctions might occur after substantial (but unknown) delays-an extinction debt. Here we explicitly couple bioclimatic envelope models of climate and habitat suitability with generic life-history models for 24 species of frogs found in the Australian Wet Tropics (AWT). We show that (i) as many as four species of frogs face imminent extinction by 2080, due primarily to climate change; (ii) three frogs face delayed extinctions; and (iii) this extinction debt will take at least a century to be realized in full. Furthermore, we find congruence between forecast rates of extinction using SARs, and demographic models with an extinction lag of 120 years. We conclude that SAR approaches can provide useful advice to conservation on climate change impacts, provided there is a good understanding of the time lags over which delayed extinctions are likely to occur. © 2016 The Author(s).

Public goods games in populations with fluctuating size.

PubMed

McAvoy, Alex; Fraiman, Nicolas; Hauert, Christoph; Wakeley, John; Nowak, Martin A

2018-05-01

Many mathematical frameworks of evolutionary game dynamics assume that the total population size is constant and that selection affects only the relative frequency of strategies. Here, we consider evolutionary game dynamics in an extended Wright-Fisher process with variable population size. In such a scenario, it is possible that the entire population becomes extinct. Survival of the population may depend on which strategy prevails in the game dynamics. Studying cooperative dilemmas, it is a natural feature of such a model that cooperators enable survival, while defectors drive extinction. Although defectors are favored for any mixed population, random drift could lead to their elimination and the resulting pure-cooperator population could survive. On the other hand, if the defectors remain, then the population will quickly go extinct because the frequency of cooperators steadily declines and defectors alone cannot survive. In a mutation-selection model, we find that (i) a steady supply of cooperators can enable long-term population survival, provided selection is sufficiently strong, and (ii) selection can increase the abundance of cooperators but reduce their relative frequency. Thus, evolutionary game dynamics in populations with variable size generate a multifaceted notion of what constitutes a trait's long-term success. Copyright © 2018 Elsevier Inc. All rights reserved.

Simulating galactic dust grain evolution on a moving mesh

NASA Astrophysics Data System (ADS)

McKinnon, Ryan; Vogelsberger, Mark; Torrey, Paul; Marinacci, Federico; Kannan, Rahul

2018-05-01

Interstellar dust is an important component of the galactic ecosystem, playing a key role in multiple galaxy formation processes. We present a novel numerical framework for the dynamics and size evolution of dust grains implemented in the moving-mesh hydrodynamics code AREPO suited for cosmological galaxy formation simulations. We employ a particle-based method for dust subject to dynamical forces including drag and gravity. The drag force is implemented using a second-order semi-implicit integrator and validated using several dust-hydrodynamical test problems. Each dust particle has a grain size distribution, describing the local abundance of grains of different sizes. The grain size distribution is discretised with a second-order piecewise linear method and evolves in time according to various dust physical processes, including accretion, sputtering, shattering, and coagulation. We present a novel scheme for stochastically forming dust during stellar evolution and new methods for sub-cycling of dust physics time-steps. Using this model, we simulate an isolated disc galaxy to study the impact of dust physical processes that shape the interstellar grain size distribution. We demonstrate, for example, how dust shattering shifts the grain size distribution to smaller sizes resulting in a significant rise of radiation extinction from optical to near-ultraviolet wavelengths. Our framework for simulating dust and gas mixtures can readily be extended to account for other dynamical processes relevant in galaxy formation, like magnetohydrodynamics, radiation pressure, and thermo-chemical processes.

The role of landscape-dependent disturbance and dispersal in metapopulation persistence.

PubMed

Elkin, Ché M; Possingham, Hugh

2008-10-01

The fundamental processes that influence metapopulation dynamics (extinction and recolonization) will often depend on landscape structure. Disturbances that increase patch extinction rates will frequently be landscape dependent such that they are spatially aggregated and have an increased likelihood of occurring in some areas. Similarly, landscape structure can influence organism movement, producing asymmetric dispersal between patches. Using a stochastic, spatially explicit model, we examine how landscape-dependent correlations between dispersal and disturbance rates influence metapopulation dynamics. Habitat patches that are situated in areas where the likelihood of disturbance is low will experience lower extinction rates and will function as partial refuges. We discovered that the presence of partial refuges increases metapopulation viability and that the value of partial refuges was contingent on whether dispersal was also landscape dependent. Somewhat counterintuitively, metapopulation viability was reduced when individuals had a preponderance to disperse away from refuges and was highest when there was biased dispersal toward refuges. Our work demonstrates that landscape structure needs to be incorporated into metapopulation models when there is either empirical data or ecological rationale for extinction and/or dispersal rates being landscape dependent.

On the probability of extinction of the Haiti cholera epidemic

NASA Astrophysics Data System (ADS)

Bertuzzo, Enrico; Finger, Flavio; Mari, Lorenzo; Gatto, Marino; Rinaldo, Andrea

2014-05-01

Nearly 3 years after its appearance in Haiti, cholera has already exacted more than 8,200 deaths and 670,000 reported cases and it is feared to become endemic. However, no clear evidence of a stable environmental reservoir of pathogenic Vibrio cholerae, the infective agent of the disease, has emerged so far, suggesting that the transmission cycle of the disease is being maintained by bacteria freshly shed by infected individuals. Thus in principle cholera could possibly be eradicated from Haiti. Here, we develop a framework for the estimation of the probability of extinction of the epidemic based on current epidemiological dynamics and health-care practice. Cholera spreading is modelled by an individual-based spatially-explicit stochastic model that accounts for the dynamics of susceptible, infected and recovered individuals hosted in different local communities connected through hydrologic and human mobility networks. Our results indicate that the probability that the epidemic goes extinct before the end of 2016 is of the order of 1%. This low probability of extinction highlights the need for more targeted and effective interventions to possibly stop cholera in Haiti.

Eco-evolutionary feedbacks drive species interactions

PubMed Central

Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio

2014-01-01

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions. PMID:24304674

Broadband Measurement of Aerosol Extinction in the Visible Range

NASA Astrophysics Data System (ADS)

He, Quanfu; Bluvshtein, Nir; Segev, Lior; Flores, Michel; Rudich, Yinon; Washenfelder, Rebecca; Brown, Steven

2017-04-01

Atmospheric aerosols influence the Earth's radiative budget directly by scattering and absorbing incoming solar radiation. Aerosol direct forcing remains one of the largest uncertainties in quantifying the role that aerosols play in the Earth's radiative budget. The optical properties of aerosols vary as a function of wavelength, but few measurements reported the wavelength dependence of aerosol extinction cross section and complex refractive indices, particularly in the blue and visible spectral range. There is also currently a large gap in our knowledge of how the optical properties evolve as a function of atmospheric aging in the visible spectrum. In this study, we constructed a new and novel laboratory instrument to measure aerosol extinction as a function of wavelength, using cavity enhanced spectroscopy with a white light source. This broadband cavity enhanced spectroscopy (BBCES) covers the 395-700 nm spectral region using a broadband light source and a grating spectrometer with charge-coupled device detector (CCD). We evaluated this BBCES by measuring extinction cross section for aerosols that are pure scattering, slightly absorbing and strongly absorbing atomized from standard materials. We also retrieved the refractive indices from the measured extinction cross sections. Secondary organic aerosols from biogenic and anthropogenic precursors were "aged" to differential time scales (1 to 10 days) in an Oxidation Flow Reactor (OFR) under the combined influence of OH, O3 and UV light. The new BBCES was used to online measure the extinction cross sections of the SOA. This talk will provide a comprehensive understanding of aerosol optical properties alerting during aging process in the 395 - 700 nm spectrum.

The Impact of Global Warming and Anoxia on Marine Benthic Community Dynamics: an Example from the Toarcian (Early Jurassic)

PubMed Central

Danise, Silvia; Twitchett, Richard J.; Little, Crispin T. S.; Clémence, Marie-Emilie

2013-01-01

The Pliensbachian-Toarcian (Early Jurassic) fossil record is an archive of natural data of benthic community response to global warming and marine long-term hypoxia and anoxia. In the early Toarcian mean temperatures increased by the same order of magnitude as that predicted for the near future; laminated, organic-rich, black shales were deposited in many shallow water epicontinental basins; and a biotic crisis occurred in the marine realm, with the extinction of approximately 5% of families and 26% of genera. High-resolution quantitative abundance data of benthic invertebrates were collected from the Cleveland Basin (North Yorkshire, UK), and analysed with multivariate statistical methods to detect how the fauna responded to environmental changes during the early Toarcian. Twelve biofacies were identified. Their changes through time closely resemble the pattern of faunal degradation and recovery observed in modern habitats affected by anoxia. All four successional stages of community structure recorded in modern studies are recognised in the fossil data (i.e. Stage III: climax; II: transitional; I: pioneer; 0: highly disturbed). Two main faunal turnover events occurred: (i) at the onset of anoxia, with the extinction of most benthic species and the survival of a few adapted to thrive in low-oxygen conditions (Stages I to 0) and (ii) in the recovery, when newly evolved species colonized the re-oxygenated soft sediments and the path of recovery did not retrace of pattern of ecological degradation (Stages I to II). The ordination of samples coupled with sedimentological and palaeotemperature proxy data indicate that the onset of anoxia and the extinction horizon coincide with both a rise in temperature and sea level. Our study of how faunal associations co-vary with long and short term sea level and temperature changes has implications for predicting the long-term effects of “dead zones” in modern oceans. PMID:23457537

The impact of global warming and anoxia on marine benthic community dynamics: an example from the Toarcian (Early Jurassic).

PubMed

Danise, Silvia; Twitchett, Richard J; Little, Crispin T S; Clémence, Marie-Emilie

2013-01-01

The Pliensbachian-Toarcian (Early Jurassic) fossil record is an archive of natural data of benthic community response to global warming and marine long-term hypoxia and anoxia. In the early Toarcian mean temperatures increased by the same order of magnitude as that predicted for the near future; laminated, organic-rich, black shales were deposited in many shallow water epicontinental basins; and a biotic crisis occurred in the marine realm, with the extinction of approximately 5% of families and 26% of genera. High-resolution quantitative abundance data of benthic invertebrates were collected from the Cleveland Basin (North Yorkshire, UK), and analysed with multivariate statistical methods to detect how the fauna responded to environmental changes during the early Toarcian. Twelve biofacies were identified. Their changes through time closely resemble the pattern of faunal degradation and recovery observed in modern habitats affected by anoxia. All four successional stages of community structure recorded in modern studies are recognised in the fossil data (i.e. Stage III: climax; II: transitional; I: pioneer; 0: highly disturbed). Two main faunal turnover events occurred: (i) at the onset of anoxia, with the extinction of most benthic species and the survival of a few adapted to thrive in low-oxygen conditions (Stages I to 0) and (ii) in the recovery, when newly evolved species colonized the re-oxygenated soft sediments and the path of recovery did not retrace of pattern of ecological degradation (Stages I to II). The ordination of samples coupled with sedimentological and palaeotemperature proxy data indicate that the onset of anoxia and the extinction horizon coincide with both a rise in temperature and sea level. Our study of how faunal associations co-vary with long and short term sea level and temperature changes has implications for predicting the long-term effects of "dead zones" in modern oceans.

Metapopulation dynamics and future persistence of epiphytic cyanolichens in a European boreal forest ecosystem

PubMed Central

Fedrowitz, Katja; Kuusinen, Mikko; Snäll, Tord

2012-01-01

1. One approach to biodiversity conservation is to set aside small woodland key habitats (WKHs) in intensively managed landscapes. The aim is to support species, such as epiphytes, which often depend on old trees and are negatively affected by intensive forestry. However, it is not known whether the number of host trees within these areas can sustain species in the long term. 2. We studied metapopulation dynamics and assessed the future persistence of epiphytes assuming host tree numbers similar to those observed in large north European WKHs. The study species were seven cyanolichens confined to Populus tremula in the boreal study area. Colonizations and extinctions were recorded in 2008 on trees that had been surveyed 13 years earlier. We applied generalized (non)linear models to test the importance of environmental conditions, facilitation and spatial connectivity on the metapopulation dynamics. We also simulated the effects of tree numbers and tree fall rates on future species persistence. 3. Metapopulation dynamics were explained by tree quality, size or tree fall. In one species, colonizations increased with increasing connectivity, and in a second species it increased if other lichens sharing the photobiont with the focal species were present, suggesting facilitation. Both stochastic extinctions from standing trees and deterministic extinctions caused by tree fall should be accounted for in projecting epiphyte metapopulation dynamics. 4. One to three infrequent, sexually dispersed study species face a significant extinction risk within 50 years, especially in areas with low tree numbers. 5. Synthesis and applications. During the coming decades, infrequent, sexually dispersed, epiphytic lichens are likely to be lost from small woodland habitat set asides in intensively managed landscapes. Local extinction will be a consequence of low colonization rates and tree fall. Low colonization rates can be prevented by retaining large trees on which lichen species colonization rates are the highest and by assuring a high density of occupied trees. The negative effect of tree fall should be compensated for by assuring continuous availability of old trees. This can be achieved by decreasing the populations of large browsers, or by retaining trees with high conservation value during management operations. PMID:22745512

Indelible Distrust: Memory Bias toward Cheaters Revealed as High Persistence against Extinction

ERIC Educational Resources Information Center

Suzuki, Atsunobu; Honma, Yoshiko; Suga, Sayaka

2013-01-01

Our ability to learn about the reputations of others--that is, who is likely to cooperate versus cheat--contributes greatly to cooperativeness in society. There has been recent debate whether humans employ memory bias favoring cheaters (i.e., there is an evolved module for the detection of cheaters) or whether no such bias exists (i.e., reputation…

Food web structure and the evolution of ecological communities

NASA Astrophysics Data System (ADS)

Quince, Christopher; Higgs, Paul G.; McKane, Alan J.

Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food web. The equations account for competition between species for the same resources, and for the diet choice of predators between alternative prey according to an evolutionarily stable strategy. The set of species present undergoes long-term evolution d ue to speciation and extinction events. We summarize results obtained on the macro-evolutionary dynamics of speciations and extinctions, and on the statistical properties of the food webs that are generated by the model. Simulations begin from small numbers of species and build up to larger webs with relatively constant species number on average. The rate of origination and extinction of species are relatively high, but remain roughly balanced throughout the simulations. When a 'parent' species undergoes sp eciation, the 'child' species usually adds to the same trophic level as the parent. The chance of the child species surviving is significantly higher if the parent is on the second or third trophic level than if it is on the first level, most likely due to a wider choice of possible prey for species on higher levels. Addition of a new species sometimes causes extinction of existing species. The parent species has a high probability of extinction because it has strong competition with the new species. Non-pa rental competitors of the new species also have a significantly higher extinction probability than average, as do prey of the new species. Predators of the new species are less likely than average to become extinct.

A stochastic model for transmission, extinction and outbreak of Escherichia coli O157:H7 in cattle as affected by ambient temperature and cleaning practices.

PubMed

Wang, Xueying; Gautam, Raju; Pinedo, Pablo J; Allen, Linda J S; Ivanek, Renata

2014-08-01

Many infectious agents transmitting through a contaminated environment are able to persist in the environment depending on the temperature and sanitation determined rates of their replication and clearance, respectively. There is a need to elucidate the effect of these factors on the infection transmission dynamics in terms of infection outbreaks and extinction while accounting for the random nature of the process. Also, it is important to distinguish between the true and apparent extinction, where the former means pathogen extinction in both the host and the environment while the latter means extinction only in the host population. This study proposes a stochastic-differential equation model as an approximation to a Markov jump process model, using Escherichia coli O157:H7 in cattle as a model system. In the model, the host population infection dynamics are described using the standard susceptible-infected-susceptible framework, and the E. coli O157:H7 population in the environment is represented by an additional variable. The backward Kolmogorov equations that determine the probability distribution and the expectation of the first passage time are provided in a general setting. The outbreak and apparent extinction of infection are investigated by numerically solving the Kolmogorov equations for the probability density function of the associated process and the expectation of the associated stopping time. The results provide insight into E. coli O157:H7 transmission and apparent extinction, and suggest ways for controlling the spread of infection in a cattle herd. Specifically, this study highlights the importance of ambient temperature and sanitation, especially during summer.

THE EXTREMELY RED HOST GALAXY OF GRB 080207

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunt, Leslie; Cresci, Giovanni; Palazzi, Eliana

2011-08-01

We present optical, near-infrared, and Spitzer IRAC and MIPS observations of the host galaxy of the dark Swift gamma-ray burst GRB 080207. The host is faint, with extremely red optical-infrared colors (R - K = 6.3, 24 {mu}m/R-band flux {approx}1000) making it an extremely red object (ERO) and a dust-obscured galaxy (DOG). The spectral energy distribution (SED) shows the clear signature of the 1.6 {mu}m photometric 'bump', typical of evolved stellar populations. We use this bump to establish the photometric redshift z{sub phot} as 2.2{sup +0.2}{sub -0.3}, using a vast library of SED templates, including M 82. The star formationmore » rate (SFR) inferred from the SED fitting is {approx}119 M{sub sun} yr{sup -1}, the stellar mass 3 x 10{sup 11} M{sub sun}, and A{sub V} extinction from 1 to 2 mag. The ERO and DOG nature of the host galaxy of the dark GRB 080207 may be emblematic of a distinct class of dark GRB hosts, with high SFRs, evolved and metal-rich stellar populations, and significant dust extinction within the host galaxy.« less

Expansion or extinction: deterministic and stochastic two-patch models with Allee effects.

PubMed

Kang, Yun; Lanchier, Nicolas

2011-06-01

We investigate the impact of Allee effect and dispersal on the long-term evolution of a population in a patchy environment. Our main focus is on whether a population already established in one patch either successfully invades an adjacent empty patch or undergoes a global extinction. Our study is based on the combination of analytical and numerical results for both a deterministic two-patch model and a stochastic counterpart. The deterministic model has either two, three or four attractors. The existence of a regime with exactly three attractors only appears when patches have distinct Allee thresholds. In the presence of weak dispersal, the analysis of the deterministic model shows that a high-density and a low-density populations can coexist at equilibrium in nearby patches, whereas the analysis of the stochastic model indicates that this equilibrium is metastable, thus leading after a large random time to either a global expansion or a global extinction. Up to some critical dispersal, increasing the intensity of the interactions leads to an increase of both the basin of attraction of the global extinction and the basin of attraction of the global expansion. Above this threshold, for both the deterministic and the stochastic models, the patches tend to synchronize as the intensity of the dispersal increases. This results in either a global expansion or a global extinction. For the deterministic model, there are only two attractors, while the stochastic model no longer exhibits a metastable behavior. In the presence of strong dispersal, the limiting behavior is entirely determined by the value of the Allee thresholds as the global population size in the deterministic and the stochastic models evolves as dictated by their single-patch counterparts. For all values of the dispersal parameter, Allee effects promote global extinction in terms of an expansion of the basin of attraction of the extinction equilibrium for the deterministic model and an increase of the probability of extinction for the stochastic model.

Theories of Lethal Mutagenesis: From Error Catastrophe to Lethal Defection.

PubMed

Tejero, Héctor; Montero, Francisco; Nuño, Juan Carlos

2016-01-01

RNA viruses get extinct in a process called lethal mutagenesis when subjected to an increase in their mutation rate, for instance, by the action of mutagenic drugs. Several approaches have been proposed to understand this phenomenon. The extinction of RNA viruses by increased mutational pressure was inspired by the concept of the error threshold. The now classic quasispecies model predicts the existence of a limit to the mutation rate beyond which the genetic information of the wild type could not be efficiently transmitted to the next generation. This limit was called the error threshold, and for mutation rates larger than this threshold, the quasispecies was said to enter into error catastrophe. This transition has been assumed to foster the extinction of the whole population. Alternative explanations of lethal mutagenesis have been proposed recently. In the first place, a distinction is made between the error threshold and the extinction threshold, the mutation rate beyond which a population gets extinct. Extinction is explained from the effect the mutation rate has, throughout the mutational load, on the reproductive ability of the whole population. Secondly, lethal defection takes also into account the effect of interactions within mutant spectra, which have been shown to be determinant for the understanding the extinction of RNA virus due to an augmented mutational pressure. Nonetheless, some relevant issues concerning lethal mutagenesis are not completely understood yet, as so survival of the flattest, i.e. the development of resistance to lethal mutagenesis by evolving towards mutationally more robust regions of sequence space, or sublethal mutagenesis, i.e., the increase of the mutation rate below the extinction threshold which may boost the adaptability of RNA virus, increasing their ability to develop resistance to drugs (including mutagens). A better design of antiviral therapies will still require an improvement of our knowledge about lethal mutagenesis.

Does red noise increase or decrease extinction risk? Single extreme events versus series of unfavorable conditions.

PubMed

Schwager, Monika; Johst, Karin; Jeltsch, Florian

2006-06-01

Recent theoretical studies have shown contrasting effects of temporal correlation of environmental fluctuations (red noise) on the risk of population extinction. It is still debated whether and under which conditions red noise increases or decreases extinction risk compared with uncorrelated (white) noise. Here, we explain the opposing effects by introducing two features of red noise time series. On the one hand, positive autocorrelation increases the probability of series of poor environmental conditions, implying increasing extinction risk. On the other hand, for a given time period, the probability of at least one extremely bad year ("catastrophe") is reduced compared with white noise, implying decreasing extinction risk. Which of these two features determines extinction risk depends on the strength of environmental fluctuations and the sensitivity of population dynamics to these fluctuations. If extreme (catastrophic) events can occur (strong noise) or sensitivity is high (overcompensatory density dependence), then temporal correlation decreases extinction risk; otherwise, it increases it. Thus, our results provide a simple explanation for the contrasting previous findings and are a crucial step toward a general understanding of the effect of noise color on extinction risk.

The threshold of a stochastic delayed SIR epidemic model with vaccination

NASA Astrophysics Data System (ADS)

Liu, Qun; Jiang, Daqing

2016-11-01

In this paper, we study the threshold dynamics of a stochastic delayed SIR epidemic model with vaccination. We obtain sufficient conditions for extinction and persistence in the mean of the epidemic. The threshold between persistence in the mean and extinction of the stochastic system is also obtained. Compared with the corresponding deterministic model, the threshold affected by the white noise is smaller than the basic reproduction number Rbar0 of the deterministic system. Results show that time delay has important effects on the persistence and extinction of the epidemic.

Collapse of an ecological network in Ancient Egypt

PubMed Central

Yeakel, Justin D.; Pires, Mathias M.; Rudolf, Lars; Koch, Paul L.; Guimarães, Paulo R.; Gross, Thilo

2014-01-01

The dynamics of ecosystem collapse are fundamental to determining how and why biological communities change through time, as well as the potential effects of extinctions on ecosystems. Here, we integrate depictions of mammals from Egyptian antiquity with direct lines of paleontological and archeological evidence to infer local extinctions and community dynamics over a 6,000-y span. The unprecedented temporal resolution of this dataset enables examination of how the tandem effects of human population growth and climate change can disrupt mammalian communities. We show that the extinctions of mammals in Egypt were nonrandom and that destabilizing changes in community composition coincided with abrupt aridification events and the attendant collapses of some complex societies. We also show that the roles of species in a community can change over time and that persistence is predicted by measures of species sensitivity, a function of local dynamic stability. To our knowledge, our study is the first high-resolution analysis of the ecological impacts of environmental change on predator–prey networks over millennial timescales and sheds light on the historical events that have shaped modern animal communities. PMID:25201967

High-precision timeline for Earth’s most severe extinction

PubMed Central

Burgess, Seth D.; Bowring, Samuel; Shen, Shu-zhong

2014-01-01

The end-Permian mass extinction was the most severe loss of marine and terrestrial biota in the last 542 My. Understanding its cause and the controls on extinction/recovery dynamics depends on an accurate and precise age model. U-Pb zircon dates for five volcanic ash beds from the Global Stratotype Section and Point for the Permian-Triassic boundary at Meishan, China, define an age model for the extinction and allow exploration of the links between global environmental perturbation, carbon cycle disruption, mass extinction, and recovery at millennial timescales. The extinction occurred between 251.941 ± 0.037 and 251.880 ± 0.031 Mya, an interval of 60 ± 48 ka. Onset of a major reorganization of the carbon cycle immediately precedes the initiation of extinction and is punctuated by a sharp (3‰), short-lived negative spike in the isotopic composition of carbonate carbon. Carbon cycle volatility persists for ∼500 ka before a return to near preextinction values. Decamillenial to millennial level resolution of the mass extinction and its aftermath will permit a refined evaluation of the relative roles of rate-dependent processes contributing to the extinction, allowing insight into postextinction ecosystem expansion, and establish an accurate time point for evaluating the plausibility of trigger and kill mechanisms. PMID:24516148

High-precision timeline for Earth's most severe extinction.

PubMed

Burgess, Seth D; Bowring, Samuel; Shen, Shu-zhong

2014-03-04

The end-Permian mass extinction was the most severe loss of marine and terrestrial biota in the last 542 My. Understanding its cause and the controls on extinction/recovery dynamics depends on an accurate and precise age model. U-Pb zircon dates for five volcanic ash beds from the Global Stratotype Section and Point for the Permian-Triassic boundary at Meishan, China, define an age model for the extinction and allow exploration of the links between global environmental perturbation, carbon cycle disruption, mass extinction, and recovery at millennial timescales. The extinction occurred between 251.941 ± 0.037 and 251.880 ± 0.031 Mya, an interval of 60 ± 48 ka. Onset of a major reorganization of the carbon cycle immediately precedes the initiation of extinction and is punctuated by a sharp (3‰), short-lived negative spike in the isotopic composition of carbonate carbon. Carbon cycle volatility persists for ∼500 ka before a return to near preextinction values. Decamillenial to millennial level resolution of the mass extinction and its aftermath will permit a refined evaluation of the relative roles of rate-dependent processes contributing to the extinction, allowing insight into postextinction ecosystem expansion, and establish an accurate time point for evaluating the plausibility of trigger and kill mechanisms.

Dynamics of origination and extinction in the marine fossil record

PubMed Central

Alroy, John

2008-01-01

The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The new data show that two biotic mechanisms have hastened recoveries from mass extinctions and confined diversity to a relatively narrow range over the past 500 million years (Myr). First, a drop in diversity of any size correlates with low extinction rates immediately afterward, so much so that extinction would almost come to a halt if diversity dropped by 90%. Second, very high extinction rates are followed by equally high origination rates. The two relationships predict that the rebound from the current mass extinction will take at least 10 Myr, and perhaps 40 Myr if it rivals the Permo-Triassic catastrophe. Regardless, any large event will result in a dramatic ecological and taxonomic restructuring of the biosphere. The data also confirm that extinction and origination rates both declined through the Phanerozoic and that several extinctions in addition to the Permo-Triassic event were particularly severe. However, the trend may be driven by taxonomic biases and the rates vary in accord with a simple log normal distribution, so there is no sharp distinction between background and mass extinctions. Furthermore, the lack of any significant autocorrelation in the data is inconsistent with macroevolutionary theories of periodicity or self-organized criticality. PMID:18695240

A cross-immunization model for the extinction of old influenza strains.

PubMed

Uekermann, Florian; Sneppen, Kim

2016-05-13

Given the frequent mutation of antigenic features, the constancy of genetic and antigenic diversity of influenza within a subtype is surprising. While the emergence of new strains and antigenic features is commonly attributed to selection by the human immune system, the mechanism that ensures the extinction of older strains remains controversial. To replicate this dynamics of replacement current models utilize mechanisms such as short-lived strain-transcending immunity, a direct competition for hosts, stochastic extinction or constrained antigenic evolution. Building on the idea of short-lived immunity we introduce a minimal model that exhibits the aforementioned dynamics of replacement. Our model relies only on competition due to an antigen specific immune-response in an unconstrained antigenic space. Furthermore the model explains the size of typical influenza epidemics as well as the tendency that new epidemics are associated with mutations of old antigens.

Invasion, Coexistence, and Extinction Driven by Preemptive Competition and Sex Ratio

NASA Astrophysics Data System (ADS)

Molnar, Ferenc; Caraco, Thomas; Korniss, Gyorgy

2012-02-01

We investigate competitive invasion in a simple population dynamics model, where females can differ genetically in the sex ratio of their offspring, and males can differ in mortality. Analyzing of the mean-field dynamics, we obtain conditions for ecological stability of a given sex-ratio allele for any mortality rate parameters. We also found that stable coexistence of the two alleles is possible, but only males can differ; one female phenotype is present. Our results show that the success of invasion is determined by the female birth sex ratio. A lower female ratio never excludes a larger female sex ratio; in case of coexistence, the surviving female phenotype always has the greater female sex ratio. Finally, we identified an interesting invasion-to-extinction scenario: successful invasion followed by extinction occurs when the invader initially propagates with the resident allele, but after excluding the resident, cannot survive on its own.

Sea level regulated tetrapod diversity dynamics through the Jurassic/Cretaceous interval

PubMed Central

Tennant, Jonathan P.; Mannion, Philip D.; Upchurch, Paul

2016-01-01

Reconstructing deep time trends in biodiversity remains a central goal for palaeobiologists, but our understanding of the magnitude and tempo of extinctions and radiations is confounded by uneven sampling of the fossil record. In particular, the Jurassic/Cretaceous (J/K) boundary, 145 million years ago, remains poorly understood, despite an apparent minor extinction and the radiation of numerous important clades. Here we apply a rigorous subsampling approach to a comprehensive tetrapod fossil occurrence data set to assess the group's macroevolutionary dynamics through the J/K transition. Although much of the signal is exclusively European, almost every higher tetrapod group was affected by a substantial decline across the boundary, culminating in the extinction of several important clades and the ecological release and radiation of numerous modern tetrapod groups. Variation in eustatic sea level was the primary driver of these patterns, controlling biodiversity through availability of shallow marine environments and via allopatric speciation on land. PMID:27587285

Starburst clusters in the Galactic center

NASA Astrophysics Data System (ADS)

Habibi, Maryam

2014-09-01

The central region of the Galaxy is the most active site of star formation in the Milky Way, where massive stars have formed very recently and are still forming today. The rich population of massive stars in the Galactic center provide a unique opportunity to study massive stars in their birth environment and probe their initial mass function, which is the spectrum of stellar masses at their birth. The Arches cluster is the youngest among the three massive clusters in the Galactic center, providing a collection of high-mass stars and a very dense core which makes this cluster an excellent site to address questions about massive star formation, the stellar mass function and the dynamical evolution of massive clusters in the Galactic center. In this thesis, I perform an observational study of the Arches cluster using K_{s}-band imaging obtained with NAOS/CONICA at the VLT combined with Subaru/Cisco J-band data to gain a full understanding of the cluster mass distribution out to its tidal radius for the first time. Since the light from the Galactic center reaches us through the Galactic disc, the extinction correction is crucial when studying this region. I use a Bayesian method to construct a realistic extinction map of the cluster. It is shown in this study that the determination of the mass of the most massive star in the Arches cluster, which had been used in previous studies to establish an upper mass limit for the star formation process in the Milky Way, strongly depends on the assumed slope of the extinction law. Assuming the two regimes of widely used infrared extinction laws, I show that the difference can reach up to 30% for individually derived stellar masses and Δ A_{Ks}˜ 1 magnitude in acquired K_{s}-band extinction, while the present-day mass function slope changes by ˜ 0.17 dex. The present-day mass function slope derived assuming the more recent extinction law, which suggests a steeper wavelength dependence for the infrared extinction law, reveals an overpopulation of massive stars in the core (r<0.2 pc) with a flat slope of α_{Nishi}=-1.50 ±0.35 in comparison to the Salpeter slope of α=-2.3. The slope of the mass function increases to α_{Nishi}=-2.21 ±0.27 in the intermediate annulus (0.2

When Local Extinction and Colonization of River Fishes Can Be Predicted by Regional Occupancy: the Role of Spatial Scales

PubMed Central

Bergerot, Benjamin; Hugueny, Bernard; Belliard, Jérôme

2013-01-01

Background Predicting which species are likely to go extinct is perhaps one of the most fundamental yet challenging tasks for conservation biologists. This is particularly relevant for freshwater ecosystems which tend to have the highest proportion of species threatened with extinction. According to metapopulation theories, local extinction and colonization rates of freshwater subpopulations can depend on the degree of regional occupancy, notably due to rescue effects. However, relationships between extinction, colonization, regional occupancy and the spatial scales at which they operate are currently poorly known. Methods And Findings: We used a large dataset of freshwater fish annual censuses in 325 stream reaches to analyse how annual extinction/colonization rates of subpopulations depend on the regional occupancy of species. For this purpose, we modelled the regional occupancy of 34 fish species over the whole French river network and we tested how extinction/colonization rates could be predicted by regional occupancy described at five nested spatial scales. Results show that extinction and colonization rates depend on regional occupancy, revealing existence a rescue effect. We also find that these effects are scale dependent and their absolute contribution to colonization and extinction tends to decrease from river section to larger basin scales. Conclusions In terms of management, we show that regional occupancy quantification allows the evaluation of local species extinction/colonization dynamics and reduction of local extinction risks for freshwater fish species implies the preservation of suitable habitats at both local and drainage basin scales. PMID:24367636

When local extinction and colonization of river fishes can be predicted by regional occupancy: the role of spatial scales.

PubMed

Bergerot, Benjamin; Hugueny, Bernard; Belliard, Jérôme

2013-01-01

Predicting which species are likely to go extinct is perhaps one of the most fundamental yet challenging tasks for conservation biologists. This is particularly relevant for freshwater ecosystems which tend to have the highest proportion of species threatened with extinction. According to metapopulation theories, local extinction and colonization rates of freshwater subpopulations can depend on the degree of regional occupancy, notably due to rescue effects. However, relationships between extinction, colonization, regional occupancy and the spatial scales at which they operate are currently poorly known. And Findings: We used a large dataset of freshwater fish annual censuses in 325 stream reaches to analyse how annual extinction/colonization rates of subpopulations depend on the regional occupancy of species. For this purpose, we modelled the regional occupancy of 34 fish species over the whole French river network and we tested how extinction/colonization rates could be predicted by regional occupancy described at five nested spatial scales. Results show that extinction and colonization rates depend on regional occupancy, revealing existence a rescue effect. We also find that these effects are scale dependent and their absolute contribution to colonization and extinction tends to decrease from river section to larger basin scales. In terms of management, we show that regional occupancy quantification allows the evaluation of local species extinction/colonization dynamics and reduction of local extinction risks for freshwater fish species implies the preservation of suitable habitats at both local and drainage basin scales.

Dynamics of a stochastic delayed SIR epidemic model with vaccination and double diseases driven by Lévy jumps

NASA Astrophysics Data System (ADS)

Liu, Qun; Jiang, Daqing; Shi, Ningzhong; Hayat, Tasawar

2018-02-01

In this paper, we study the dynamics of a stochastic delayed SIR epidemic model with vaccination and double diseases which make the research more complex. The environment variability in this paper is characterized by white noise and Lévy noise. We establish sufficient conditions for extinction and persistence in the mean of the two epidemic diseases. It is shown that: (i) time delay and Lévy noise have important effects on the persistence and extinction of epidemic diseases; (ii) two diseases can coexist under certain conditions.

Dynamic Blowout Risk Analysis Using Loss Functions.

PubMed

Abimbola, Majeed; Khan, Faisal

2018-02-01

Most risk analysis approaches are static; failing to capture evolving conditions. Blowout, the most feared accident during a drilling operation, is a complex and dynamic event. The traditional risk analysis methods are useful in the early design stage of drilling operation while falling short during evolving operational decision making. A new dynamic risk analysis approach is presented to capture evolving situations through dynamic probability and consequence models. The dynamic consequence models, the focus of this study, are developed in terms of loss functions. These models are subsequently integrated with the probability to estimate operational risk, providing a real-time risk analysis. The real-time evolving situation is considered dependent on the changing bottom-hole pressure as drilling progresses. The application of the methodology and models are demonstrated with a case study of an offshore drilling operation evolving to a blowout. © 2017 Society for Risk Analysis.

The impact of rapid evolution on population dynamics in the wild: experimental test of eco-evolutionary dynamics.

PubMed

Turcotte, Martin M; Reznick, David N; Hare, J Daniel

2011-11-01

Rapid evolution challenges the assumption that evolution is too slow to impact short-term ecological dynamics. This insight motivates the study of 'Eco-Evolutionary Dynamics' or how evolution and ecological processes reciprocally interact on short time scales. We tested how rapid evolution impacts concurrent population dynamics using an aphid (Myzus persicae) and an undomesticated host (Hirschfeldia incana) in replicated wild populations. We manipulated evolvability by creating non-evolving (single clone) and potentially evolving (two-clone) aphid populations that contained genetic variation in intrinsic growth rate. We observed significant evolution in two-clone populations whether or not they were exposed to predators and competitors. Evolving populations grew up to 42% faster and attained up to 67% higher density, compared with non-evolving control populations but only in treatments exposed to competitors and predators. Increased density also correlates with relative fitness of competing clones suggesting a full eco-evolutionary dynamic cycle defined as reciprocal interactions between evolution and density. © 2011 Blackwell Publishing Ltd/CNRS.

Sensory Cortical Population Dynamics Uniquely Track Behavior across Learning and Extinction

PubMed Central

Katz, Donald B.

2014-01-01

Neural responses in many cortical regions encode information relevant to behavior: information that necessarily changes as that behavior changes with learning. Although such responses are reasonably theorized to be related to behavior causation, the true nature of that relationship cannot be clarified by simple learning studies, which show primarily that responses change with experience. Neural activity that truly tracks behavior (as opposed to simply changing with experience) will not only change with learning but also change back when that learning is extinguished. Here, we directly probed for this pattern, recording the activity of ensembles of gustatory cortical single neurons as rats that normally consumed sucrose avidly were trained first to reject it (i.e., conditioned taste aversion learning) and then to enjoy it again (i.e., extinction), all within 49 h. Both learning and extinction altered cortical responses, consistent with the suggestion (based on indirect evidence) that extinction is a novel form of learning. But despite the fact that, as expected, postextinction single-neuron responses did not resemble “naive responses,” ensemble response dynamics changed with learning and reverted with extinction: both the speed of stimulus processing and the relationships among ensemble responses to the different stimuli tracked behavioral relevance. These data suggest that population coding is linked to behavior with a fidelity that single-neuron coding is not. PMID:24453316

Historical data as a baseline for conservation: reconstructing long-term faunal extinction dynamics in Late Imperial–modern China

PubMed Central

Turvey, Samuel T.; Crees, Jennifer J.; Di Fonzo, Martina M. I.

2015-01-01

Extinction events typically represent extended processes of decline that cannot be reconstructed using short-term studies. Long-term archives are necessary to determine past baselines and the extent of human-caused biodiversity change, but the capacity of historical datasets to provide predictive power for conservation must be assessed within a robust analytical framework. Local Chinese gazetteers represent a more than 400-year country-level dataset containing abundant information on past environmental conditions and include extensive records of gibbons, which have a restricted present-day distribution but formerly occurred across much of China. Gibbons show pre-twentieth century range contraction, with significant fragmentation by the mid-eighteenth century and population loss escalating in the late nineteenth century. Isolated gibbon populations persisted for about 40 years before local extinction. Populations persisted for longer at higher elevations, and disappeared earlier from northern and eastern regions, with the biogeography of population loss consistent with the contagion model of range collapse in response to human demographic expansion spreading directionally across China. The long-term Chinese historical record can track extinction events and human interactions with the environment across much longer timescales than are usually addressed in ecology, contributing novel baselines for conservation and an increased understanding of extinction dynamics and species vulnerability or resilience to human pressures. PMID:26246553

Historical data as a baseline for conservation: reconstructing long-term faunal extinction dynamics in Late Imperial-modern China.

PubMed

Turvey, Samuel T; Crees, Jennifer J; Di Fonzo, Martina M I

2015-08-22

Extinction events typically represent extended processes of decline that cannot be reconstructed using short-term studies. Long-term archives are necessary to determine past baselines and the extent of human-caused biodiversity change, but the capacity of historical datasets to provide predictive power for conservation must be assessed within a robust analytical framework. Local Chinese gazetteers represent a more than 400-year country-level dataset containing abundant information on past environmental conditions and include extensive records of gibbons, which have a restricted present-day distribution but formerly occurred across much of China. Gibbons show pre-twentieth century range contraction, with significant fragmentation by the mid-eighteenth century and population loss escalating in the late nineteenth century. Isolated gibbon populations persisted for about 40 years before local extinction. Populations persisted for longer at higher elevations, and disappeared earlier from northern and eastern regions, with the biogeography of population loss consistent with the contagion model of range collapse in response to human demographic expansion spreading directionally across China. The long-term Chinese historical record can track extinction events and human interactions with the environment across much longer timescales than are usually addressed in ecology, contributing novel baselines for conservation and an increased understanding of extinction dynamics and species vulnerability or resilience to human pressures. © 2015 The Authors.

Vocal specialization through tracheal elongation in an extinct Miocene pheasant from China.

PubMed

Li, Zhiheng; Clarke, Julia A; Eliason, Chad M; Stidham, Thomas A; Deng, Tao; Zhou, Zhonghe

2018-05-25

Modifications to the upper vocal tract involving hyper-elongated tracheae have evolved many times within crown birds, and their evolution has been linked to a 'size exaggeration' hypothesis in acoustic signaling and communication, whereby smaller-sized birds can produce louder sounds. A fossil skeleton of a new extinct species of wildfowl (Galliformes: Phasianidae) from the late Miocene of China, preserves an elongated, coiled trachea that represents the oldest fossil record of this vocal modification in birds and the first documentation of its evolution within pheasants. The phylogenetic position of this species within Phasianidae has not been fully resolved, but appears to document a separate independent origination of this vocal modification within Galliformes. The fossil preserves a coiled section of the trachea and other remains supporting a tracheal length longer than the bird's body. This extinct species likely produced vocalizations with a lower fundamental frequency and reduced harmonics compared to similarly-sized pheasants. The independent evolution of this vocal feature in galliforms living in both open and closed habitats does not appear to be correlated with other factors of biology or its open savanna-like habitat. Features present in the fossil that are typically associated with sexual dimorphism suggest that sexual selection may have resulted in the evolution of both the morphology and vocalization mechanism in this extinct species.

Asymmetric competition impacts evolutionary rescue in a changing environment.

PubMed

Van Den Elzen, Courtney L; Kleynhans, Elizabeth J; Otto, Sarah P

2017-06-28

Interspecific competition can strongly influence the evolutionary response of a species to a changing environment, impacting the chance that the species survives or goes extinct. Previous work has shown that when two species compete for a temporally shifting resource distribution, the species lagging behind the resource peak is the first to go extinct due to competitive exclusion. However, this work assumed symmetrically distributed resources and competition. Asymmetries can generate differences between species in population sizes, genetic variation and trait means. We show that asymmetric resource availability or competition can facilitate coexistence and even occasionally cause the leading species to go extinct first. Surprisingly, we also find cases where traits evolve in the opposite direction to the changing environment because of a 'vacuum of competitive release' created when the lagging species declines in number. Thus, the species exhibiting the slowest rate of trait evolution is not always the most likely to go extinct in a changing environment. Our results demonstrate that the extent to which species appear to be tracking environmental change and the extent to which they are preadapted to that change may not necessarily determine which species will be the winners and which will be the losers in a rapidly changing world. © 2017 The Author(s).

Speciations and Extinctions in a Self-Organizing Critical Model of Tree-Like Evolution

NASA Astrophysics Data System (ADS)

Kramer, M.; Vandewalle, N.; Ausloos, M.

1996-04-01

We study analytically a simple model of a self-organized critical evolution. The model considers both extinction and speciation events leading to the growth of phylogenetic-like trees. Through a mean-field like theory, we study the evolution of the local configurations for the tree leaves. The fitness threshold, below which life activity takes place through avalanches of all sizes is calculated. The transition between speciating (evolving) and dead trees is obtained and is in agreement with numerical simulations. Moreover, this theoretical work suggests that the structure of the tree is strongly dependent on the extinction strength. Nous étudions analytiquement un modèle simple d'évolution auto-organisée critique. Le modèle considère des extinctions et des spéciations conduisant à une croissance d'arbre phylogénétiques. Nous étudions ici par une théorie de champ moyen l'évolution des configurations des extrémités de l'arbre. Le seuil critique de “fitness” en-dessous duquel des explosions d'activité biologique de toutes tailles se produisent est calculé. La transition entre arbres croissants et arbres éteints est également obtenue en accord avec les simulations. En outre, ce travail théorique suggère que la structure des arbres générés dépend fortement du paramètre d'extinctions.

Influence of climate drivers on colonization and extinction dynamics of wetland-dependent species

USGS Publications Warehouse

Ray, Andrew M.; Gould, William R.; Hossack, Blake R.; Sepulveda, Adam; Thoma, David P.; Patla, Debra A.; Daley, Rob; Al-Chokhachy, Robert K.

2016-01-01

Freshwater wetlands are particularly vulnerable to climate change. Specifically, changes in temperature, precipitation, and evapotranspiration (i.e., climate drivers) are likely to alter flooding regimes of wetlands and affect the vital rates, abundance, and distributions of wetland-dependent species. Amphibians may be among the most climate-sensitive wetland-dependent groups, as many species rely on shallow or intermittently flooded wetland habitats for breeding. Here, we integrated multiple years of high-resolution gridded climate and amphibian monitoring data from Grand Teton and Yellowstone National Parks to explicitly model how variations in climate drivers and habitat conditions affect the occurrence and breeding dynamics (i.e., annual extinction and colonization rates) of amphibians. Our results showed that models incorporating climate drivers outperformed models of amphibian breeding dynamics that were exclusively habitat based. Moreover, climate-driven variation in extinction rates, but not colonization rates, disproportionately influenced amphibian occupancy in monitored wetlands. Long-term monitoring from national parks coupled with high-resolution climate data sets will be crucial to describing population dynamics and characterizing the sensitivity of amphibians and other wetland-dependent species to climate change. Further, long-term monitoring of wetlands in national parks will help reduce uncertainty surrounding wetland resources and strengthen opportunities to make informed, science-based decisions that have far-reaching benefits.

Modeling the within-host dynamics of cholera: bacterial-viral interaction.

PubMed

Wang, Xueying; Wang, Jin

2017-08-01

Novel deterministic and stochastic models are proposed in this paper for the within-host dynamics of cholera, with a focus on the bacterial-viral interaction. The deterministic model is a system of differential equations describing the interaction among the two types of vibrios and the viruses. The stochastic model is a system of Markov jump processes that is derived based on the dynamics of the deterministic model. The multitype branching process approximation is applied to estimate the extinction probability of bacteria and viruses within a human host during the early stage of the bacterial-viral infection. Accordingly, a closed-form expression is derived for the disease extinction probability, and analytic estimates are validated with numerical simulations. The local and global dynamics of the bacterial-viral interaction are analysed using the deterministic model, and the result indicates that there is a sharp disease threshold characterized by the basic reproduction number [Formula: see text]: if [Formula: see text], vibrios ingested from the environment into human body will not cause cholera infection; if [Formula: see text], vibrios will grow with increased toxicity and persist within the host, leading to human cholera. In contrast, the stochastic model indicates, more realistically, that there is always a positive probability of disease extinction within the human host.

Shape matters: Lifecycle of cooperative patches promotes cooperation in bulky populations

PubMed Central

Misevic, Dusan; Frénoy, Antoine; Lindner, Ariel B; Taddei, François

2015-01-01

Natural cooperative systems take many forms, ranging from one-dimensional cyanobacteria arrays to fractal-like biofilms. We use in silico experimental systems to study a previously overlooked factor in the evolution of cooperation, physical shape of the population. We compare the emergence and maintenance of cooperation in populations of digital organisms that inhabit bulky (100 × 100 cells) or slender (4 × 2500) toroidal grids. Although more isolated subpopulations of secretors in a slender population could be expected to favor cooperation, we find the opposite: secretion evolves to higher levels in bulky populations. We identify the mechanistic explanation for the shape effect by analyzing the lifecycle and dynamics of cooperator patches, from their emergence and growth, to invasion by noncooperators and extinction. Because they are constrained by the population shape, the cooperator patches expand less in slender than in bulky populations, leading to fewer cooperators, less public good secretion, and generally lower cooperation. The patch dynamics and mechanisms of shape effect are robust across several digital cooperation systems and independent of the underlying basis for cooperation (public good secretion or a cooperation game). Our results urge for a greater consideration of population shape in the study of the evolution of cooperation across experimental and modeling systems. PMID:25639379

Extinction risk in successional landscapes subject to catastrophic disturbances.

Treesearch

David Boughton; Urmila Malvadkar

2002-01-01

We explore the thesis that stochasticity in successional-disturbance systems can be an agent of species extinction. The analysis uses a simple model of patch dynamics for seral stages in an idealized landscape; each seral stage is assumed to support a specialist biota. The landscape as a whole is characterized by a mean patch birth rate, mean patch size, and mean...

STATUS OF THE RELICT LEOPARD FROG (RANA ONCA): OUR LIMITED UNDERSTANDING OF THE DISTRIBUTION, SIZE, AND DYNAMICS OF EXTANT AND RECENTLY EXTINCT POPULATIONS

EPA Science Inventory

The relict leopard frog (Rana onca) was once thought to be extinct, but has recently been shown to comprise a valid taxon with extant populations. Here, we discuss research from several studies, conducted between 1991 and 200 1, that represent the basis for our understanding of t...

'Tales of Symphonia': extinction dynamics in response to past climate change in Madagascan rainforests.

PubMed

Virah-Sawmy, Malika; Bonsall, Michael B; Willis, Katherine J

2009-12-23

Madagascar's rainforests are among the most biodiverse in the world. Understanding the population dynamics of important species within these forests in response to past climatic variability provides valuable insight into current and future species composition. Here, we use a population-level approach to analyse palaeoecological records over the last 5300 years to understand how populations of Symphonia cf. verrucosa became locally extinct in some rainforest fragments along the southeast coast of Madagascar in response to rapid climate change, yet persisted in others. Our results indicate that regional (climate) variability contributed to synchronous decline of S. cf. verrucosa populations in these forests. Superimposed on regional fluctuations were local processes that could have contributed or mitigated extinction. Specifically, in the forest with low soil nutrients, population model predictions indicated that there was coexistence between S. cf. verrucosa and Erica spp., but in the nutrient-rich forest, interspecific effects between Symphonia and Erica spp. may have pushed Symphonia to extinction at the peak of climatic change. We also demonstrate that Symphonia is a good indicator of a threshold event, exhibiting erratic fluctuations prior to and long after the critical climatic point has passed.

Climate change in metacommunities: dispersal gives double-sided effects on persistence.

PubMed

Eklöf, Anna; Kaneryd, Linda; Münger, Peter

2012-11-05

Climate change is increasingly affecting the structure and dynamics of ecological communities both at local and at regional scales, and this can be expected to have important consequences for their robustness and long-term persistence. The aim of the present work is to analyse how the spatial structure of the landscape and dispersal patterns of species (dispersal rate and average dispersal distance) affects metacommunity response to two disturbances: (i) increased mortality during dispersal and (ii) local species extinction. We analyse the disturbances both in isolation and in combination. Using a spatially and dynamically explicit metacommunity model, we find that the effect of dispersal on metacommunity persistence is two-sided: on the one hand, high dispersal significantly reduces the risk of bottom-up extinction cascades following the local removal of a species; on the other hand, when dispersal imposes a risk to the dispersing individuals, high dispersal increases extinction risks, especially when dispersal is global. Large-bodied species with long generation times at the highest trophic level are particularly vulnerable to extinction when dispersal involves a risk. This suggests that decreasing the mortality risk of dispersing individuals by improving the quality of the habitat matrix may greatly increase the robustness of metacommunities.

Metapopulation Dynamics of the Mistletoe and Its Host in Savanna Areas with Different Fire Occurrence

PubMed Central

Teodoro, Grazielle Sales; van den Berg, Eduardo; Arruda, Rafael

2013-01-01

Mistletoes are aerial hemiparasitic plants which occupy patches of favorable habitat (host trees) surrounded by unfavorable habitat and may be possibly modeled as a metapopulation. A metapopulation is defined as a subdivided population that persists due to the balance between colonization and extinction in discrete habitat patches. Our aim was to evaluate the dynamics of the mistletoe Psittacanthus robustus and its host Vochysia thyrsoidea in three Brazilian savanna areas using a metapopulation approach. We also evaluated how the differences in terms of fire occurrence affected the dynamic of those populations (two areas burned during the study and one was fire protected). We monitored the populations at six-month intervals. P. robustus population structure and dynamics met the expected criteria for a metapopulation: i) the suitable habitats for the mistletoe occur in discrete patches; (ii) local populations went extinct during the study and (iii) colonization of previously non-occupied patches occurred. The ratio of occupied patches decreased in all areas with time. Local mistletoe populations went extinct due to two different causes: patch extinction in area with no fire and fire killing in the burned areas. In a burned area, the largest decrease of occupied patch ratios occurred due to a fire event that killed the parasites without, however, killing the host trees. The greatest mortality of V. thyrsoidea occurred in the area without fire. In this area, all the dead trees supported mistletoe individuals and no mortality was observed for parasite-free trees. Because P. robustus is a fire sensitive species and V. thyrsoidea is fire tolerant, P. robustus seems to increase host mortality, but its effect is lessened by periodic burning that reduces the parasite loads. PMID:23776554

Sustainability of virulence in a phage-bacterial ecosystem.

PubMed

Heilmann, Silja; Sneppen, Kim; Krishna, Sandeep

2010-03-01

Virulent phages and their bacterial hosts represent an unusual sort of predator-prey system where each time a prey is eaten, hundreds of new predators are born. It is puzzling how, despite the apparent effectiveness of the phage predators, they manage to avoid driving their bacterial prey to extinction. Here we consider a phage-bacterial ecosystem on a two-dimensional (2-d) surface and show that homogeneous space in itself enhances coexistence. We analyze different behavioral mechanisms that can facilitate coexistence in a spatial environment. For example, we find that when the latent times of the phage are allowed to evolve, selection favors "mediocre killers," since voracious phage rapidly deplete local resources and go extinct. Our model system thus emphasizes the differences between short-term proliferation and long-term ecosystem sustainability.

Extinction and recolonization of coastal megafauna following human arrival in New Zealand.

PubMed

Collins, Catherine J; Rawlence, Nicolas J; Prost, Stefan; Anderson, Christian N K; Knapp, Michael; Scofield, R Paul; Robertson, Bruce C; Smith, Ian; Matisoo-Smith, Elizabeth A; Chilvers, B Louise; Waters, Jonathan M

2014-07-07

Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction-replacement event in penguins (Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record.

PubMed

Silvestro, Daniele; Cascales-Miñana, Borja; Bacon, Christine D; Antonelli, Alexandre

2015-07-01

Plants have a long evolutionary history, during which mass extinction events dramatically affected Earth's ecosystems and its biodiversity. The fossil record can shed light on the diversification dynamics of plant life and reveal how changes in the origination-extinction balance have contributed to shaping the current flora. We use a novel Bayesian approach to estimate origination and extinction rates in plants throughout their history. We focus on the effect of the 'Big Five' mass extinctions and on estimating the timing of origin of vascular plants, seed plants and angiosperms. Our analyses show that plant diversification is characterized by several shifts in origination and extinction rates, often matching the most important geological boundaries. The estimated origin of major plant clades predates the oldest macrofossils when considering the uncertainties associated with the fossil record and the preservation process. Our findings show that the commonly recognized mass extinctions have affected each plant group differently and that phases of high extinction often coincided with major floral turnovers. For instance, after the Cretaceous-Paleogene boundary we infer negligible shifts in diversification of nonflowering seed plants, but find significantly decreased extinction in spore-bearing plants and increased origination rates in angiosperms, contributing to their current ecological and evolutionary dominance. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Extinction and recolonization of coastal megafauna following human arrival in New Zealand

PubMed Central

Collins, Catherine J.; Rawlence, Nicolas J.; Prost, Stefan; Anderson, Christian N. K.; Knapp, Michael; Scofield, R. Paul; Robertson, Bruce C.; Smith, Ian; Matisoo-Smith, Elizabeth A.; Chilvers, B. Louise; Waters, Jonathan M.

2014-01-01

Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction–replacement event in penguins (Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction. PMID:24827440

Relict or colonizer? Extinction and range expansion of penguins in southern New Zealand

PubMed Central

Boessenkool, Sanne; Austin, Jeremy J.; Worthy, Trevor H.; Scofield, Paul; Cooper, Alan; Seddon, Philip J.; Waters, Jonathan M.

2008-01-01

Recent human expansion into the Pacific initiated a dramatic avian extinction crisis, and surviving taxa are typically interpreted as declining remnants of previously abundant populations. As a case in point, New Zealand's endangered yellow-eyed penguin (Megadyptes antipodes) is widely considered to have been more abundant and widespread in the past. By contrast, our genetic and morphological analyses of prehistoric, historic and modern penguin samples reveal that this species expanded its range to the New Zealand mainland only in the last few hundred years. This range expansion was apparently facilitated by the extinction of M. antipodes' previously unrecognized sister species following Polynesian settlement in New Zealand. Based on combined genetic and morphological data, we describe this new penguin species, the first known to have suffered human-mediated extinction. The range expansion of M. antipodes so soon after the extinction of its sister species supports a historic paradigmatic shift in New Zealand Polynesian culture. Additionally, such a dynamic biological response to human predation reveals a surprising and less recognized potential for species to have benefited from the extinction of their ecologically similar sister taxa and highlights the complexity of large-scale extinction events. PMID:19019791

METAPOPULATION DYNAMICS AND AMPHIBIAN CONSERVATION

EPA Science Inventory

In many respects, amphibian spatial dynamics resemble classical metapopulation models, where subpopulations in breeding ponds blink in and out of existance and where extinction and colonization rates are functions of pond spatial arrangement. This "ponds-as-patches" view of amphi...

Biostratigraphy and chronostratigraphy of the Cambrian-Ordovician great American carbonate bank

USGS Publications Warehouse

Taylor, John F.; Repetski, John E.; Loch, James D.; Leslie, Stephen A.

2012-01-01

The carbonate strata of the great American carbonate bank (GACB) have been subdivided and correlated with ever-increasing precision and accuracy during the past half century through use of the dominant organisms that evolved on the Laurentian platform through the Cambrian and the Ordovician. Trilobites and conodonts remain the primary groups used for this purpose, although brachiopods, both calcareous and phosphatic, and graptolites are very important in certain facies and intervals. A series of charts show the chronostratigraphic units (series and stages) currently in use for deposits of the GACB and the biostratigraphic units (zones, subzones, and biomeres) whose boundaries delineate them. Older and, in some cases obsolete, stages and faunal units are included in the figures to allow users to relate information from previous publications and/or industry databases to modern units. This chapter also provides a brief discussion on the use of biostratigraphy in the recognition and interregional correlation of supersequence boundaries within the Sauk and Tippecanoe megasequences, and the varied perspectives on the nature of biostratigraphic units and their defining taxa during the past half century. Also included are a concise update on the biomere concept, and an explanation of the biostratigraphic consequences of a profound change in the dynamics of extinction and replacement that occurred on the GACB in the Early Ordovician when the factors responsible for platformwide biomere-type extinctions faded and ultimately disappeared. A final section addresses recent and pending refinements in the genus and species taxonomy of biostratigraphically significant fossil groups, the potential they hold for greatly improved correlation, and the obstacles to be overcome for that potential to be realized.

Species-area relationships and extinction forecasts.

PubMed

Halley, John M; Sgardeli, Vasiliki; Monokrousos, Nikolaos

2013-05-01

The species-area relationship (SAR) predicts that smaller areas contain fewer species. This is the basis of the SAR method that has been used to forecast large numbers of species committed to extinction every year due to deforestation. The method has a number of issues that must be handled with care to avoid error. These include the functional form of the SAR, the choice of equation parameters, the sampling procedure used, extinction debt, and forest regeneration. Concerns about the accuracy of the SAR technique often cite errors not much larger than the natural scatter of the SAR itself. Such errors do not undermine the credibility of forecasts predicting large numbers of extinctions, although they may be a serious obstacle in other SAR applications. Very large errors can arise from misinterpretation of extinction debt, inappropriate functional form, and ignoring forest regeneration. Major challenges remain to understand better the relationship between sampling protocol and the functional form of SARs and the dynamics of relaxation, especially in continental areas, and to widen the testing of extinction forecasts. © 2013 New York Academy of Sciences.

Impact Crises, Mass Extinctions, and Galactic Dynamics: A Unified Theory

NASA Technical Reports Server (NTRS)

Rampino, M.R.

1997-01-01

A general hypothesis linking mass extinctions of life with impacts of large asteroids and comets is based on astronomical data, impact dynamics, and geological information. The waiting times of large-body impacts on the Earth, derived from the flux of Earth-crossing asteroids and comets, and the estimated size of impacts capable of causing large-scale environmental disasters predict that impacts of objects (sup 3)5 km in diameter ((sup 3)10(exp 7) Mt TNT equivalent) could be sufficient to explain the record of about 25 extinction pulses in the last 540 m.y., with the five recorded major mass extinctions related to the impacts of the largest objects of (sup 3)10 km in diameter ( (sup 3)10(exp 8) Mt events). Smaller impacts (about 10(exp 6)-10(exp 7) Mt), with significant regional and even global environmental effects, could be responsible for the lesser boundaries in the geologic record. Tests of the "kill curve" relationship for impact-induced extinctions based on new data on extinction intensities and several well-dated large impact craters suggest that major mass extinctions require large impacts, and that a step in the kill curve may exist at impacts that produce craters of -100 km diameter, with smaller impacts capable of only relatively weak extinction pulses. Single impact craters < about 60 km in diameter should not be associated with global extinction pulses detectable in the Sepkoski database (although they may explain stage and zone boundaries marked by lesser faunal turnover), but multiple impacts in that size range may produce significant stepped extinction pulses. Statistical tests of the last occurrences of species at mass-extinction boundaries are generally consistent with predictions for abrupt or stepped extinctions, and several boundaries are known to show "catastrophic" signatures of environmental disasters and biomass crash, impoverished postextinction fauna and flora dominated by stress-tolerant and opportunistic species, and gradual ecological recovery and radiation of new taxa. Isotopic and other geochemical signatures are also generally consistent with the expected after-effects of catastrophic impacts. Seven of the recognized extinction pulses are associated with concurrent (in some cases multiple) stratigraphic impact markers (e.g., layers with high Ir, shocked minerals, microtektites), and/or large, dated impact craters. Other less-well-studied crisis intervals show elevated Ir, still well below that of the K/T spike, which might be explained by low-Ir impactors, ejecta blowoff, or the sedimentary reworking and dilution of impact signatures. The best explanation for a possible periodic component of about 30 m.y. in mass extinctions and clusters of impacts is the modulation of the comet flux associated with the solar system's periodic passage through the plane of the Milky Way Galaxy. The quantitative agreement among paleontological, geological, and astronomical data suggests an important underlying unification of the processes involved.

Hierarchical competition models with the Allee effect II: the case of immigration.

PubMed

Assas, Laila; Dennis, Brian; Elaydi, Saber; Kwessi, Eddy; Livadiotis, George

2015-01-01

This is part II of an earlier paper that dealt with hierarchical models with the Allee effect but with no immigration. In this paper, we greatly simplify the proofs in part I and provide a proof of the global dynamics of the non-hyperbolic cases that were previously conjectured. Then, we show how immigration to one of the species or to both would, drastically, change the dynamics of the system. It is shown that if the level of immigration to one or to both species is above a specified level, then there will be no extinction region where both species go to extinction.

Diversification dynamics and transoceanic Eurasian-Australian disjunction in the genus Picris (Compositae) induced by the interplay of shifts in intrinsic/extrinsic traits and paleoclimatic oscillations.

PubMed

Slovák, Marek; Kučera, Jaromír; Lack, Hans Walter; Ziffer-Berger, Jotham; Melicharková, Andrea; Záveská, Eliška; Vďačný, Peter

2018-02-01

Understanding transcontinental biogeographic patterns has been one of the main foci of the field of biogeography. While multiple explanations for transcontinental disjunctions have been proposed, little is still known about the relative importance of intrinsic and extrinsic traits for the diversification dynamics of disjunct taxa. Here, we study the evolutionary history of the genus Picris L. (Compositae), a great model for investigating the diversification dynamics of transoceanic bipolar disjunct organisms. Ancestral state reconstructions indicate that the most recent common ancestor (MRCA) of Picris was a semelparous and heterocarpic herb that lived in unpredictable environments of North Africa and West Asia. Diversification analyses suggest a significant shift in speciation ca. 1 million years ago, likely associated with the onset of the mid-Pleistocene revolution. Longevity characters are correlated with the evolution of particular fruit types and with environmental conditions. Heterocarpic species are mostly semelparous herbs strongly linked with unpredictable habitats, while homocarpic taxa are mostly iteroparous plants occurring in predictable environments. Binary-state speciation and extinction analyses suggest that homocarpy, iteroparity, and habitats predictability accelerate diversification. Although the combination of homocarpy and iteroparity evolved in several lineages, only members of the P. hieracioides group were able to colonise Eurasia and expand to Australia by transoceanic dispersal. Those findings indicate that large-scale colonisation events depend on a complex interplay of intrinsic and extrinsic factors. Copyright © 2017 Elsevier Inc. All rights reserved.

Understory Bird Communities in Amazonian Rainforest Fragments: Species Turnover through 25 Years Post-Isolation in Recovering Landscapes

PubMed Central

Stouffer, Philip C.; Johnson, Erik I.; Bierregaard, Richard O.; Lovejoy, Thomas E.

2011-01-01

Inferences about species loss following habitat conversion are typically drawn from short-term surveys, which cannot reconstruct long-term temporal dynamics of extinction and colonization. A long-term view can be critical, however, to determine the stability of communities within fragments. Likewise, landscape dynamics must be considered, as second growth structure and overall forest cover contribute to processes in fragments. Here we examine bird communities in 11 Amazonian rainforest fragments of 1–100 ha, beginning before the fragments were isolated in the 1980s, and continuing through 2007. Using a method that accounts for imperfect detection, we estimated extinction and colonization based on standardized mist-net surveys within discreet time intervals (1–2 preisolation samples and 4–5 post-isolation samples). Between preisolation and 2007, all fragments lost species in an area-dependent fashion, with loss of as few as <10% of preisolation species from 100-ha fragments, but up to 70% in 1-ha fragments. Analysis of individual time intervals revealed that the 2007 result was not due to gradual species loss beginning at isolation; both extinction and colonization occurred in every time interval. In the last two samples, 2000 and 2007, extinction and colonization were approximately balanced. Further, 97 of 101 species netted before isolation were detected in at least one fragment in 2007. Although a small subset of species is extremely vulnerable to fragmentation, and predictably goes extinct in fragments, developing second growth in the matrix around fragments encourages recolonization in our landscapes. Species richness in these fragments now reflects local turnover, not long-term attrition of species. We expect that similar processes could be operating in other fragmented systems that show unexpectedly low extinction. PMID:21731616

Understory bird communities in Amazonian rainforest fragments: species turnover through 25 years post-isolation in recovering landscapes.

PubMed

Stouffer, Philip C; Johnson, Erik I; Bierregaard, Richard O; Lovejoy, Thomas E

2011-01-01

Inferences about species loss following habitat conversion are typically drawn from short-term surveys, which cannot reconstruct long-term temporal dynamics of extinction and colonization. A long-term view can be critical, however, to determine the stability of communities within fragments. Likewise, landscape dynamics must be considered, as second growth structure and overall forest cover contribute to processes in fragments. Here we examine bird communities in 11 Amazonian rainforest fragments of 1-100 ha, beginning before the fragments were isolated in the 1980s, and continuing through 2007. Using a method that accounts for imperfect detection, we estimated extinction and colonization based on standardized mist-net surveys within discreet time intervals (1-2 preisolation samples and 4-5 post-isolation samples). Between preisolation and 2007, all fragments lost species in an area-dependent fashion, with loss of as few as <10% of preisolation species from 100-ha fragments, but up to 70% in 1-ha fragments. Analysis of individual time intervals revealed that the 2007 result was not due to gradual species loss beginning at isolation; both extinction and colonization occurred in every time interval. In the last two samples, 2000 and 2007, extinction and colonization were approximately balanced. Further, 97 of 101 species netted before isolation were detected in at least one fragment in 2007. Although a small subset of species is extremely vulnerable to fragmentation, and predictably goes extinct in fragments, developing second growth in the matrix around fragments encourages recolonization in our landscapes. Species richness in these fragments now reflects local turnover, not long-term attrition of species. We expect that similar processes could be operating in other fragmented systems that show unexpectedly low extinction.

Meteors, space aliens, and other exotic encounters

Treesearch

Tom Hofacker

1998-01-01

Exotics have had a big impact on our environment. If you do not think so, just look at how many people believe that humans would not exist on this planet were it not for exotics. This belief centers on two main theories: (1) that humans could not have evolved were it not for a huge meteor from outer space striking the earth resulting in extinction of the dinasours, the...

Lateral plate evolution in the threespine stickleback: getting nowhere fast.

PubMed

Bell, M A

2001-01-01

Gasterosteus aculeatus is a small Holarctic fish with marine, anadromous, and freshwater populations. Marine and anadromous populations apparently have changed little in the past 10 million years and exhibit limited geographical variation. In contrast, freshwater isolates have been founded repeatedly by marine and anadromous populations, and post-glacial isolates have undergone extraordinary adaptive radiation. Stickleback traits that have diversified during post-glacial radiation, including the 'lateral plates' (LP), can evolve substantially within decades after colonization of fresh water or when the environment (particularly predation regime) changes. Although highly divergent freshwater isolates of G. aculeatus have existed for at least 10 million years, they have rarely experienced sustained evolutionary divergence leading to formation of widespread, phenotypically distinct species. The paradox of rapid LP evolution without sustained divergence has resulted from selective extinction of highly divergent populations, because they are specialized for conditions in small, isolated habitats that tend to dry up within limited periods. Biological species of G. aculeatus may also evolve within decades, and are also prone to extinction because they are endemic to and specialized for small, ephemeral habitats. The high rate of evolution observed in contemporary threespine stickleback populations may not be unique to this species complex and has important implications for use of post-glacial populations in comparative studies, speciation rate, and discrimination of sympatric and allopatric speciation.

Assessing regional and interspecific variation in threshold responses of forest breeding birds through broad scale analyses.

PubMed

van der Hoek, Yntze; Renfrew, Rosalind; Manne, Lisa L

2013-01-01

Identifying persistence and extinction thresholds in species-habitat relationships is a major focal point of ecological research and conservation. However, one major concern regarding the incorporation of threshold analyses in conservation is the lack of knowledge on the generality and transferability of results across species and regions. We present a multi-region, multi-species approach of modeling threshold responses, which we use to investigate whether threshold effects are similar across species and regions. We modeled local persistence and extinction dynamics of 25 forest-associated breeding birds based on detection/non-detection data, which were derived from repeated breeding bird atlases for the state of Vermont. We did not find threshold responses to be particularly well-supported, with 9 species supporting extinction thresholds and 5 supporting persistence thresholds. This contrasts with a previous study based on breeding bird atlas data from adjacent New York State, which showed that most species support persistence and extinction threshold models (15 and 22 of 25 study species respectively). In addition, species that supported a threshold model in both states had associated average threshold estimates of 61.41% (SE = 6.11, persistence) and 66.45% (SE = 9.15, extinction) in New York, compared to 51.08% (SE = 10.60, persistence) and 73.67% (SE = 5.70, extinction) in Vermont. Across species, thresholds were found at 19.45-87.96% forest cover for persistence and 50.82-91.02% for extinction dynamics. Through an approach that allows for broad-scale comparisons of threshold responses, we show that species vary in their threshold responses with regard to habitat amount, and that differences between even nearby regions can be pronounced. We present both ecological and methodological factors that may contribute to the different model results, but propose that regardless of the reasons behind these differences, our results merit a warning that threshold values cannot simply be transferred across regions or interpreted as clear-cut targets for ecosystem management and conservation.

Hierarchical spatial structure of stream fish colonization and extinction

USGS Publications Warehouse

Hitt, N.P.; Roberts, J.H.

2012-01-01

Spatial variation in extinction and colonization is expected to influence community composition over time. In stream fish communities, local species richness (alpha diversity) and species turnover (beta diversity) are thought to be regulated by high extinction rates in headwater streams and high colonization rates in downstream areas. We evaluated the spatiotemporal structure of fish communities in streams originally surveyed by Burton and Odum 1945 (Ecology 26: 182-194) in Virginia, USA and explored the effects of species traits on extinction and colonization dynamics. We documented dramatic changes in fish community structure at both the site and stream scales. Of the 34 fish species observed, 20 (59%) were present in both time periods, but 11 (32%) colonized the study area and three (9%) were extirpated over time. Within streams, alpha diversity increased in two of three streams but beta diversity decreased dramatically in all streams due to fish community homogenization caused by colonization of common species and extirpation of rare species. Among streams, however, fish communities differentiated over time. Regression trees indicated that reproductive life-history traits such as spawning mound construction, associations with mound-building species, and high fecundity were important predictors of species persistence or colonization. Conversely, native fishes not associated with mound-building exhibited the highest rates of extirpation from streams. Our results demonstrate that stream fish colonization and extinction dynamics exhibit hierarchical spatial structure and suggest that mound-building fishes serve as keystone species for colonization of headwater streams.

The extinction and dust-to-gas structure of the planetary nebula NGC 7009 observed with MUSE

NASA Astrophysics Data System (ADS)

Walsh, J. R.; Monreal-Ibero, A.; Barlow, M. J.; Ueta, T.; Wesson, R.; Zijlstra, A. A.

2016-04-01

Context. Dust plays a significant role in planetary nebulae. Dust ejected with the gas in the asymptotic giant branch (AGB) phase is subject to the harsh environment of the planetary nebula (PN) while the star is evolving towards a white dwarf. Dust surviving the PN phase contributes to the dust content of the interstellar medium. Aims: The morphology of the internal dust extinction has been mapped for the first time in a PN, the bright nearby Galactic nebula NGC 7009. The morphologies of the gas, dust extinction and dust-to-gas ratio are compared to the structural features of the nebula. Methods: Emission line maps in H Balmer and Paschen lines were formed from analysis of MUSE cubes of NGC 7009 observed during science verification of the instrument. The measured electron temperature and density from the same cube were employed to predict the theoretical H line ratios and derive the extinction distribution across the nebula. After correction for the interstellar extinction to NGC 7009, the internal AV/NH has been mapped for the first time in a PN. Results: The extinction map of NGC 7009 has considerable structure, broadly corresponding to the morphological features of the nebula. The dust-to-gas ratio, AV/NH, increases from 0.7 times the interstellar value to >5 times from the centre towards the periphery of the ionized nebula. The integrated AV/NH is about 2× the mean ISM value. A large-scale feature in the extinction map is a wave, consisting of a crest and trough, at the rim of the inner shell. The nature of this feature is investigated and instrumental and physical causes considered; no convincing mechanisms were identified to produce this feature, other than AGB mass loss variations. Conclusions: Extinction mapping from H emission line imaging of PNe with MUSE provides a powerful tool for revealing the properties of internal dust and the dust-to-gas ratio. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme 060.A-9347(A).

Global Implications of late Pleistocene Megafaunal Extinctions in the Holarctic

NASA Astrophysics Data System (ADS)

Cooper, Alan; Turney, Chris

2017-04-01

Improved resolution data from radiocarbon, climate and ancient DNA studies of megafauna and humans is providing the first ability to disentangle the roles of climate change and human impact in the Late Pleistocene megafaunal extinctions. In the Holarctic we find that megafaunal populations underwent repeated local or global extinctions apparently associated with abrupt, centennial to millennial duration warming events (Dansgaard-Oeschger interstadials). Importantly, the extinction events took place both before and after the arrival of modern humans in the landscape. Here we look at the possible role of human activity in Holarctic and suggest it may be through the disruption of metapopulation processes which stabilize ecosystems and may have evolved to provide resilience to rapid and frequent climate shifts in the past. The observed relationship between climate and humans on megafaunal populations may provide a model for global extinction. Fortunately in this regard, the rapid movement of the first Native Americans throughout both American continents during the Last Deglaciation provides a powerful and unique model system for testing the competing roles on extinction because the opposing climate trends in each hemisphere at the time. Here we show that while megafaunal extinctions were associated with warming trends in both cases, the out-of-phase climate patterns caused the sequence and timing of events to be mirrored, providing a unique high-resolution view of the interactions of human colonization and rapid climate change on megafaunal ecosystems, with implications for future warming scenarios. References: Cooper, A., Turney, C., Hughen, K.A., Brook, B.W., McDonald, H.G., Bradshaw, C.J.A., 2015. Abrupt warming events drove Late Pleistocene Holarctic megafaunal turnover. Science 349, 602-606. Metcalf, J.L., Turney, C., Barnett, R., Martin, F., Bray, S.C., Vilstrup, J.T., Orlando, L., Salas-Gismondi, R., Loponte, D., Medina, M., De Nigris, M., Civalero, T., Fernández, P.M., Gasco, A., Duran, V., Seymour, K.L., Otaola, C., Gil, A., Paunero, R., Prevosti, F.J., Bradshaw, C.J.A., Wheeler, J.C., Borrero, L., Austin, J.J., Cooper, A., 2016. Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation. Science Advances 2, doi: 10.1126/sciadv.1501682.

Acute, but not chronic, exposure to d-cycloserine facilitates extinction and modulates spontaneous recovery of a conditioned taste aversion.

PubMed

Mickley, G Andrew; Remus, Jennifer L; Ramos, Linnet; Wilson, Gina N; Biesan, Orion R; Ketchesin, Kyle D

2012-01-18

D-cycloserine, the glutamate N-methyl-D-aspartate receptor partial agonist, has been reported to facilitate the extinction of learned fears acquired in both naturalistic and laboratory settings. The current study extended this literature by evaluating the ability of either chronic or acute administrations of DCS to modulate the extinction and spontaneous recovery of a conditioned taste aversion (CTA). Twenty-three hour fluid-deprived Sprague-Dawley rats acquired a strong CTA following 3 pairings of a conditioned stimulus (CS; 0.3% oral saccharin)+unconditioned stimulus [US; 81 mg/kg (i.p.) lithium chloride (LiCl)]. In separate groups of rats, we then employed 2 different extinction paradigms: (1) CS-only (CSO-EXT) in which saccharin was presented every-other day, or (2) Explicitly Unpaired (EU-EXT) in which both saccharin and LiCl were presented but on alternate days. Previous studies have indicated that the EU-EXT procedure speeds up the extinction process. Further, spontaneous recovery of a CTA emerges following CSO-EXT but the EU-EXT paradigm causes a suppression of spontaneous recovery. DCS (15 mg/kg, i.p.) was administered immediately after daily liquid presentations (saccharin or water, alternate days) during the extinction period. In an acute drug manipulation, DCS (15 mg/kg, i.p.) or saline control injections were administered for 4 days only. This was done during one of 3 different phases of extinction [i.e., static (2-5%), early dynamic (8-16%), or middle dynamic (20-40%) saccharin reacceptance]. Other animals assigned to the chronic DCS condition received daily DCS (15 mg/kg, i.p.) throughout extinction. Changes in saccharin drinking in these animals were compared to the data from rats that received no drug (saline controls). Once rats met our criterion for asymptotic extinction (90% reacceptance of the CS) they entered a 30-day latency period during which they received water for 1 h/day. The day after the completion of the latency period, a final opportunity to drink saccharin was provided (spontaneous recovery test). Saline-treated control rats that went through the EU-EXT procedure achieved asymptotic extinction more quickly than did the CSO-EXT rats and did not exhibit a spontaneous recovery of the CTA. Chronic DCS treatments did not significantly reduce the time to achieve asymptotic CTA extinction in rats exposed to either CSO or EU extinction methods. Further, animals treated with DCS throughout EU-EXT exhibited a spontaneous recovery of the CTA whereas the saline-treated, EU-EXT rats did not. Thus, chronic DCS treatment did not shorten the time to extinguish a CTA and this treatment eliminated the ability of EU-EXT to block spontaneous recovery of the CTA. Acute DCS treatments were more effective in reducing the time required to extinguish a CTA than were chronic drug treatments. Moreover, the timing of these acute DCS treatments affected spontaneous recovery of the CTA depending on the extinction method employed. Acute DCS administrations later in extinction were more effective in reducing spontaneous recovery than were early administrations if the rats went through the CSO-EXT procedure. However, late-in-extinction administrations of DCS facilitated spontaneous recovery of the CTA in rats that experienced the EU-EXT method. These data agree with other findings suggesting that DCS treatments are more effective when administered a limited number of times. Our data extend these findings to the CTA paradigm and further suggest that, depending on the extinction paradigm employed, acute exposure to DCS can speed up CTA extinction and reduce spontaneous recovery of the aversion. The timing of the acute DCS treatment during extinction is generally less important than its duration in predicting the rate of CTA extinction. However, the timing of acute DCS treatments during extinction and the method of extinction employed can interact to affect spontaneous recovery of a CTA. Copyright © 2011 Elsevier Inc. All rights reserved.

Fluctuations in epidemic modeling - disease extinction and control

NASA Astrophysics Data System (ADS)

Schwartz, Ira

2009-03-01

The analysis of infectious disease fluctuations has recently seen an increasing rise in the use of new tools and models from stochastic dynamics and statistical physics. Examples arise in modeling fluctuations of multi-strain diseases, in modeling adaptive social behavior and its impact on disease fluctuations, and in the analysis of disease extinction in finite population models. Proper stochastic model reduction [1] allows one to predict unobserved fluctuations from observed data in multi-strain models [2]. Degree alteration and power law behavior is predicted in adaptive network epidemic models [3,4]. And extinction rates derived from large fluctuation theory exhibit scaling with respect to distance to the bifurcation point of disease onset with an unusual exponent [5]. In addition to outbreak prediction, another main goal of epidemic modeling is one of eliminating the disease to extinction through various control mechanisms, such as vaccine implementation or quarantine. In this talk, a description will be presented of the fluctuational behavior of several epidemic models and their extinction rates. A general framework and analysis of the effect of non-Gaussian control actuations which enhance the rate to disease extinction will be described. In particular, in it is shown that even in the presence of a small Poisson distributed vaccination program, there is an exponentially enhanced rate to disease extinction. These ideas may lead to improved methods of controlling disease where random vaccinations are prevalent. [4pt] Recent papers:[0pt] [1] E. Forgoston and I. B. Schwartz, ``Escape Rates in a Stochastic Environment with Multiple Scales,'' arXiv:0809.1345 2008.[0pt] [2] L. B. Shaw, L. Billings, I. B. Schwartz, ``Using dimension reduction to improve outbreak predictability of multi-strain diseases,'' J. Math. Bio. 55, 1 2007.[0pt] [3] L. B. Shaw and I. B. Schwartz, ``Fluctuating epidemics on adaptive networks,'' Physical Review E 77, 066101 2008.[0pt] [4] L. B. Shaw and I. B. Schwartz, ``Noise induced dynamics in adaptivenetworks with applications to epidemiology,'' arXiv:0807.3455 2008.[0pt] [5] M. I. Dykman, I. B. Schwartz, A. S. Landsman, ``Disease Extinction in the Presence of Random Vaccination,'' Phys. Rev. Letts. 101, 078101 2008.

A general stochastic model for sporophytic self-incompatibility.

PubMed

Billiard, Sylvain; Tran, Viet Chi

2012-01-01

Disentangling the processes leading populations to extinction is a major topic in ecology and conservation biology. The difficulty to find a mate in many species is one of these processes. Here, we investigate the impact of self-incompatibility in flowering plants, where several inter-compatible classes of individuals exist but individuals of the same class cannot mate. We model pollen limitation through different relationships between mate availability and fertilization success. After deriving a general stochastic model, we focus on the simple case of distylous plant species where only two classes of individuals exist. We first study the dynamics of such a species in a large population limit and then, we look for an approximation of the extinction probability in small populations. This leads us to consider inhomogeneous random walks on the positive quadrant. We compare the dynamics of distylous species to self-fertile species with and without inbreeding depression, to obtain the conditions under which self-incompatible species can be less sensitive to extinction while they can suffer more pollen limitation. © Springer-Verlag 2011

Population turnover and adaptation in heterogeneous environments

NASA Astrophysics Data System (ADS)

Campos, Paulo R. A.; de Oliveira, Viviane M.

2012-02-01

We study adaptive dynamics in a structured population model of asexual individuals which takes into account environmental heterogeneity among the subpopulations. The key purpose of the present work is to address how population turnovers, i.e. extinction events followed by recolonization, affect the rate of fixation of advantageous mutations. This model is a generalization of our previous model to address the interplay between environmental correlation and evolutionary forces on the adaptive process. The incorporation of population turnovers into the model enables us to make a direct correspondence between the model and host-parasite dynamics (epidemiological models). Strikingly, contrary to the intuitive and usual deleterious effect associated to extinction events, it is observed that population turnovers can in fact speed up adaptation as heterogeneity rises. On the other side, in nearly homogeneous population turnovers have a neutral effect on fixation rates, but a detrimental outcome is also achieved when extinction events become very common. In resume, population turnover outcomes on fixation rates of advantageous mutations are strongly influenced by the selective correlation among the subpopulations (demes).

Antipredator defenses predict diversification rates

PubMed Central

Arbuckle, Kevin; Speed, Michael P.

2015-01-01

The “escape-and-radiate” hypothesis predicts that antipredator defenses facilitate adaptive radiations by enabling escape from constraints of predation, diversified habitat use, and subsequently speciation. Animals have evolved diverse strategies to reduce the direct costs of predation, including cryptic coloration and behavior, chemical defenses, mimicry, and advertisement of unprofitability (conspicuous warning coloration). Whereas the survival consequences of these alternative defenses for individuals are well-studied, little attention has been given to the macroevolutionary consequences of alternative forms of defense. Here we show, using amphibians as the first, to our knowledge, large-scale empirical test in animals, that there are important macroevolutionary consequences of alternative defenses. However, the escape-and-radiate hypothesis does not adequately describe them, due to its exclusive focus on speciation. We examined how rates of speciation and extinction vary across defensive traits throughout amphibians. Lineages that use chemical defenses show higher rates of speciation as predicted by escape-and-radiate but also show higher rates of extinction compared with those without chemical defense. The effect of chemical defense is a net reduction in diversification compared with lineages without chemical defense. In contrast, acquisition of conspicuous coloration (often used as warning signals or in mimicry) is associated with heightened speciation rates but unchanged extinction rates. We conclude that predictions based on the escape-and-radiate hypothesis must incorporate the effect of traits on both speciation and extinction, which is rarely considered in such studies. Our results also suggest that knowledge of defensive traits could have a bearing on the predictability of extinction, perhaps especially important in globally threatened taxa such as amphibians. PMID:26483488

Holocene extinction dynamics of Equus hydruntinus, a late-surviving European megafaunal mammal

NASA Astrophysics Data System (ADS)

Crees, Jennifer J.; Turvey, Samuel T.

2014-05-01

The European wild ass (Equus hydruntinus) is a globally extinct Eurasian equid. This species was widespread in Europe and southwest Asia during the Late Pleistocene, but its distribution became restricted to southern Europe and adjacent geographic regions in the Holocene. Previous research on E. hydruntinus has focused predominantly on its taxonomy and Late Pleistocene distribution. However, its Holocene distribution and extinction remain poorly understood, despite the fact that the European wild ass represents one of Europe's very few globally extinct Holocene megafaunal mammal species. We summarise all available Holocene zooarchaeological spatio-temporal occurrence data for the species, and analyse patterns of its distribution and extinction using point pattern analysis (kernel density estimation and Clark Evans index) and optimal linear estimation. We demonstrate that the geographic range of E. hydruntinus became highly fragmented into discrete subpopulations during the Holocene, which were associated with separate regions of open habitat and which became progressively extinct between the Neolithic and Iron Age. These data challenge previous suggestions of the late survival of E. hydruntinus into the medieval period in Spain, and instead suggest that postglacial climate-driven vegetational changes were a primary factor responsible for extinction of the species, driving isolation of small remnant subpopulations that may have been increasingly vulnerable to human exploitation. This study contributes to a more nuanced understanding of Late Quaternary species extinctions in Eurasia, suggesting that they were temporally staggered and distinct in their respective extinction trajectories.

Scaling rules for the final decline to extinction

PubMed Central

Griffen, Blaine D.; Drake, John M.

2009-01-01

Space–time scaling rules are ubiquitous in ecological phenomena. Current theory postulates three scaling rules that describe the duration of a population's final decline to extinction, although these predictions have not previously been empirically confirmed. We examine these scaling rules across a broader set of conditions, including a wide range of density-dependent patterns in the underlying population dynamics. We then report on tests of these predictions from experiments using the cladoceran Daphnia magna as a model. Our results support two predictions that: (i) the duration of population persistence is much greater than the duration of the final decline to extinction and (ii) the duration of the final decline to extinction increases with the logarithm of the population's estimated carrying capacity. However, our results do not support a third prediction that the duration of the final decline scales inversely with population growth rate. These findings not only support the current standard theory of population extinction but also introduce new empirical anomalies awaiting a theoretical explanation. PMID:19141422

When did Carcharocles megalodon become extinct? A new analysis of the fossil record.

PubMed

Pimiento, Catalina; Clements, Christopher F

2014-01-01

Carcharocles megalodon ("Megalodon") is the largest shark that ever lived. Based on its distribution, dental morphology, and associated fauna, it has been suggested that this species was a cosmopolitan apex predator that fed on marine mammals from the middle Miocene to the Pliocene (15.9-2.6 Ma). Prevailing theory suggests that the extinction of apex predators affects ecosystem dynamics. Accordingly, knowing the time of extinction of C. megalodon is a fundamental step towards understanding the effects of such an event in ancient communities. However, the time of extinction of this important species has never been quantitatively assessed. Here, we synthesize the most recent records of C. megalodon from the literature and scientific collections and infer the date of its extinction by making a novel use of the Optimal Linear Estimation (OLE) model. Our results suggest that C. megalodon went extinct around 2.6 Ma. Furthermore, when contrasting our results with known ecological and macroevolutionary trends in marine mammals, it became evident that the modern composition and function of modern gigantic filter-feeding whales was established after the extinction of C. megalodon. Consequently, the study of the time of extinction of C. megalodon provides the basis to improve our understanding of the responses of marine species to the removal of apex predators, presenting a deep-time perspective for the conservation of modern ecosystems.

When Did Carcharocles megalodon Become Extinct? A New Analysis of the Fossil Record

PubMed Central

Pimiento, Catalina; Clements, Christopher F.

2014-01-01

Carcharocles megalodon (“Megalodon”) is the largest shark that ever lived. Based on its distribution, dental morphology, and associated fauna, it has been suggested that this species was a cosmopolitan apex predator that fed on marine mammals from the middle Miocene to the Pliocene (15.9–2.6 Ma). Prevailing theory suggests that the extinction of apex predators affects ecosystem dynamics. Accordingly, knowing the time of extinction of C. megalodon is a fundamental step towards understanding the effects of such an event in ancient communities. However, the time of extinction of this important species has never been quantitatively assessed. Here, we synthesize the most recent records of C. megalodon from the literature and scientific collections and infer the date of its extinction by making a novel use of the Optimal Linear Estimation (OLE) model. Our results suggest that C. megalodon went extinct around 2.6 Ma. Furthermore, when contrasting our results with known ecological and macroevolutionary trends in marine mammals, it became evident that the modern composition and function of modern gigantic filter-feeding whales was established after the extinction of C. megalodon. Consequently, the study of the time of extinction of C. megalodon provides the basis to improve our understanding of the responses of marine species to the removal of apex predators, presenting a deep-time perspective for the conservation of modern ecosystems. PMID:25338197

Dynamics of Droplet Extinction in Slow Convective Flows

NASA Technical Reports Server (NTRS)

Nayagam, V.; Haggard, J. B., Jr.; Williams, F. A.

1999-01-01

The classical model for droplet combustion predicts that the square of the droplet diameter decreases linearly with time. It also predicts that a droplet of any size will burn to completion over a period of time. However, it has been known for some time that under certain conditions flames surrounding a droplet, in a quiescent environment, could extinguish because of insufficient residence time for the chemistry to proceed to completion. This type of extinction that occurs for smaller droplets has been studied extensively in the past. Large droplets, on the other hand, exhibit a different type of extinction where excessive radiative heat loss from the flame zone leads to extinction. This mode of "radiative extinction" was theoretically predicted for droplet burning by Chao et al. and was observed in recent space experiments in a quiescent environment. Thus far, the fundamental flammability limit prescribed by radiative extinction of liquid droplets has been measured only under quiescent environmental conditions. In many space platforms, however, ventilation systems produce small convective flows and understanding of the influences of this convection on the extinction process will help better define the radiative extinction flammability boundaries. Boundaries defined by experiments and captured using theoretical models could provide enhanced fire safety margin in space explor1999063d investigation of convective effects will help in interpretations of burning-rate data obtained during free-floated droplet combustion experiments with small residual velocities.

Flame Dynamics and Chemistry in LRE Combustion Instability

DTIC Science & Technology

2016-12-22

simulation conditions are as follows: the upper boundary consists of a mixture of DME, oxygen and nitrogen at a fixed temperature of 300 K, while the lower...Fig. 11 a. However, the reduction effect of increased oxygen con- centration on the cool flame extinction temperature is again over- predicted by... temperature chemistry and extends the hysteresis between ignition and Fig. 11. Ignition and extinction temperatures at various strain rates and oxygen

An allometric approach to quantify the extinction vulnerability of birds and mammals.

PubMed

Hilbers, J P; Schipper, A M; Hendriks, A J; Verones, F; Pereira, H M; Huijbregts, M A J

2016-03-01

Methods to quantify the vulnerability of species to extinction are typically limited by the availability of species-specific input data pertaining to life-history characteristics and population dynamics. This lack of data hampers global biodiversity assessments and conservation planning. Here, we developed a new framework that systematically quantifies extinction risk based on allometric relationships between various wildlife demographic parameters and body size. These allometric relationships have a solid theoretical and ecological foundation. Extinction risk indicators included are (1) the probability of extinction, (2) the mean time to extinction, and (3) the critical patch size. We applied our framework to assess the global extinction vulnerability of terrestrial carnivorous and non-carnivorous birds and mammals. Irrespective of the indicator used, large-bodied species were found to be more vulnerable to extinction than their smaller counterparts. The patterns with body size were confirmed for all species groups by a comparison with IUCN data on the proportion of extant threatened species: the models correctly predicted a multimodal distribution with body size for carnivorous birds and a monotonic distribution for mammals and non-carnivorous birds. Carnivorous mammals were found to have higher extinction risks than non-carnivores, while birds were more prone to extinction than mammals. These results are explained by the allometric relationships, predicting the vulnerable species groups to have lower intrinsic population growth rates, smaller population sizes, lower carrying capacities, or larger dispersal distances, which, in turn, increase the importance of losses due to environmental stochastic effects and dispersal activities. Our study is the first to integrate population viability analysis and allometry into a novel, process-based framework that is able to quantify extinction risk of a large number of species without requiring data-intensive, species-specific information. The framework facilitates the estimation of extinction vulnerabilities of data-deficient species. It may be applied to forecast extinction vulnerability in response to a changing environment, by incorporating quantitative relationships between wildlife demographic parameters and environmental drivers like habitat alteration, climate change, or hunting.

Species sorting and patch dynamics in harlequin metacommunities affect the relative importance of environment and space.

PubMed

Leibold, Mathew A; Loeuille, Nicolas

2015-12-01

Metacommunity theory indicates that variation in local community structure can be partitioned into components including those related to local environmental conditions vs. spatial effects and that these can be quantified using statistical methods based on variation partitioning. It has been hypothesized that joint associations of community composition with environment and space could be due to patch dynamics involving colonization-extinction processes in environmentally heterogeneous landscapes but this has yet to be theoretically shown. We develop a two-patch, type-two, species competition model in such a "harlequin" landscape (where different patches have different environments) to evaluate how composition is related to environmental and spatial effects as a function of background extinction rate. Using spatially implicit analytical models, we find that the environmental association of community composition declines with extinction rate as expected. Using spatially explicit simulation models, we further find that there is an increase in the spatial structure with extinction due to spatial patterning into clusters that are not related to environmental conditions but that this increase is limited. Natural metacommunities often show both environment and spatial determination even under conditions of relatively high isolation and these could be more easily explained by our model than alternative metacommunity models.

Adapted conservation measures are required to save the Iberian lynx in a changing climate

NASA Astrophysics Data System (ADS)

Fordham, D. A.; Akçakaya, H. R.; Brook, B. W.; Rodríguez, A.; Alves, P. C.; Civantos, E.; Triviño, M.; Watts, M. J.; Araújo, M. B.

2013-10-01

The Iberian lynx (Lynx pardinus) has suffered severe population declines in the twentieth century and is now on the brink of extinction. Climate change could further threaten the survival of the species, but its forecast effects are being neglected in recovery plans. Quantitative estimates of extinction risk under climate change have so far mostly relied on inferences from correlative projections of species' habitat shifts. Here we use ecological niche models coupled to metapopulation simulations with source-sink dynamics to directly investigate the combined effects of climate change, prey availability and management intervention on the persistence of the Iberian lynx. Our approach is unique in that it explicitly models dynamic bi-trophic species interactions in a climate change setting. We show that anticipated climate change will rapidly and severely decrease lynx abundance and probably lead to its extinction in the wild within 50 years, even with strong global efforts to mitigate greenhouse gas emissions. In stark contrast, we also show that a carefully planned reintroduction programme, accounting for the effects of climate change, prey abundance and habitat connectivity, could avert extinction of the lynx this century. Our results demonstrate, for the first time, why considering prey availability, climate change and their interaction in models is important when designing policies to prevent future biodiversity loss.

Mathematical Modeling of Extinction of Inhomogeneous Populations

PubMed Central

Karev, G.P.; Kareva, I.

2016-01-01

Mathematical models of population extinction have a variety of applications in such areas as ecology, paleontology and conservation biology. Here we propose and investigate two types of sub-exponential models of population extinction. Unlike the more traditional exponential models, the life duration of sub-exponential models is finite. In the first model, the population is assumed to be composed clones that are independent from each other. In the second model, we assume that the size of the population as a whole decreases according to the sub-exponential equation. We then investigate the “unobserved heterogeneity”, i.e. the underlying inhomogeneous population model, and calculate the distribution of frequencies of clones for both models. We show that the dynamics of frequencies in the first model is governed by the principle of minimum of Tsallis information loss. In the second model, the notion of “internal population time” is proposed; with respect to the internal time, the dynamics of frequencies is governed by the principle of minimum of Shannon information loss. The results of this analysis show that the principle of minimum of information loss is the underlying law for the evolution of a broad class of models of population extinction. Finally, we propose a possible application of this modeling framework to mechanisms underlying time perception. PMID:27090117

Sustainability of Virulence in a Phage-Bacterial Ecosystem ▿ †

PubMed Central

Heilmann, Silja; Sneppen, Kim; Krishna, Sandeep

2010-01-01

Virulent phages and their bacterial hosts represent an unusual sort of predator-prey system where each time a prey is eaten, hundreds of new predators are born. It is puzzling how, despite the apparent effectiveness of the phage predators, they manage to avoid driving their bacterial prey to extinction. Here we consider a phage-bacterial ecosystem on a two-dimensional (2-d) surface and show that homogeneous space in itself enhances coexistence. We analyze different behavioral mechanisms that can facilitate coexistence in a spatial environment. For example, we find that when the latent times of the phage are allowed to evolve, selection favors “mediocre killers,” since voracious phage rapidly deplete local resources and go extinct. Our model system thus emphasizes the differences between short-term proliferation and long-term ecosystem sustainability. PMID:20071588

Unique parasite aDNA in moa coprolites from New Zealand suggests mass parasite extinctions followed human-induced megafauna extinctions

USGS Publications Warehouse

Lafferty, Kevin D.; Hopkins, Skylar R.

2018-01-01

Having split early from Gondwana, Zealandia (now modern New Zealand) escaped discovery until the late 13th century, and therefore remains an important glimpse into a human-free world. Without humans or other land mammals, diverse and peculiar birds evolved in isolation, including several flightless moa species, the giant pouakai eagle (Harpagornis moorei), the kiwi (Apteryx mantelli), and the kakapo parrot (Strigops habroptila). This unique community has fascinated paleoecologists, who have spent almost two centuries devising new ways to glean information from ancient bird remains. In PNAS, Boast et al. (1) apply one recent technological advance, ancient DNA (aDNA) metabarcoding, to confirm previous discoveries and report new details about moa and kakapo diets, parasites, and niches. Their efforts confirm Zealandia was a lot different before humans arrived.

The Origin and Diversification of Birds.

PubMed

Brusatte, Stephen L; O'Connor, Jingmai K; Jarvis, Erich D

2015-10-05

Birds are one of the most recognizable and diverse groups of modern vertebrates. Over the past two decades, a wealth of new fossil discoveries and phylogenetic and macroevolutionary studies has transformed our understanding of how birds originated and became so successful. Birds evolved from theropod dinosaurs during the Jurassic (around 165-150 million years ago) and their classic small, lightweight, feathered, and winged body plan was pieced together gradually over tens of millions of years of evolution rather than in one burst of innovation. Early birds diversified throughout the Jurassic and Cretaceous, becoming capable fliers with supercharged growth rates, but were decimated at the end-Cretaceous extinction alongside their close dinosaurian relatives. After the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today. Copyright © 2015 Elsevier Ltd. All rights reserved.

Learning and extinction of a passive avoidance response in mice with high levels of predisposition to catalepsy.

PubMed

Dubrovina, N I; Zinov'ev, D R; Zinov'eva, D V; Kulikov, A V

2009-06-01

This report presents results obtained from comparative analysis of learning and the dynamics of extinction of a conditioned passive avoidance response in ASC mice, which were bred for a high level of predisposition to catalepsy, and in CBA and AKR mice. The following findings were obtained: 1) impairments to the extinction of the memory of fear represent an important symptom of depression in ASC mice; 2) extinction is delayed in CBA mice; and 3) new inhibitory learning occurs quickly in AKR mice. Prolonged retention of the fear memory in ASC mice appears to be related to increased anxiety on prolonged testing without a punishment. The deficit of inhibition of the fear reaction in ASC mice allows this strain to be regarded as a genetic model of depression.

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

PubMed

Steinacher, Arno; Bates, Declan G; Akman, Ozgur E; Soyer, Orkun S

2016-01-01

Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability) under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest an explanation for the ubiquity of nonlinear dynamics in gene expression networks, and generate useful guidelines for the design of synthetic gene circuits.

Unidirectional pulmonary airflow patterns in the savannah monitor lizard.

PubMed

Schachner, Emma R; Cieri, Robert L; Butler, James P; Farmer, C G

2014-02-20

The unidirectional airflow patterns in the lungs of birds have long been considered a unique and specialized trait associated with the oxygen demands of flying, their endothermic metabolism and unusual pulmonary architecture. However, the discovery of similar flow patterns in the lungs of crocodilians indicates that this character is probably ancestral for all archosaurs--the group that includes extant birds and crocodilians as well as their extinct relatives, such as pterosaurs and dinosaurs. Unidirectional flow in birds results from aerodynamic valves, rather than from sphincters or other physical mechanisms, and similar aerodynamic valves seem to be present in crocodilians. The anatomical and developmental similarities in the primary and secondary bronchi of birds and crocodilians suggest that these structures and airflow patterns may be homologous. The origin of this pattern is at least as old as the split between crocodilians and birds, which occurred in the Triassic period. Alternatively, this pattern of flow may be even older; this hypothesis can be tested by investigating patterns of airflow in members of the outgroup to birds and crocodilians, the Lepidosauromorpha (tuatara, lizards and snakes). Here we demonstrate region-specific unidirectional airflow in the lungs of the savannah monitor lizard (Varanus exanthematicus). The presence of unidirectional flow in the lungs of V. exanthematicus thus gives rise to two possible evolutionary scenarios: either unidirectional airflow evolved independently in archosaurs and monitor lizards, or these flow patterns are homologous in archosaurs and V. exanthematicus, having evolved only once in ancestral diapsids (the clade encompassing snakes, lizards, crocodilians and birds). If unidirectional airflow is plesiomorphic for Diapsida, this respiratory character can be reconstructed for extinct diapsids, and evolved in a small ectothermic tetrapod during the Palaeozoic era at least a hundred million years before the origin of birds.

Dynamic N -occupancy models: estimating demographic rates and local abundance from detection-nondetection data

Treesearch

Sam Rossman; Charles B. Yackulic; Sarah P. Saunders; Janice Reid; Ray Davis; Elise F. Zipkin

2016-01-01

Occupancy modeling is a widely used analytical technique for assessing species distributions and range dynamics. However, occupancy analyses frequently ignore variation in abundance of occupied sites, even though site abundances affect many of the parameters being estimated (e.g., extinction, colonization, detection probability). We introduce a new model (“dynamic

Breeding Young as a Survival Strategy during Earth’s Greatest Mass Extinction

NASA Astrophysics Data System (ADS)

Botha-Brink, Jennifer; Codron, Daryl; Huttenlocker, Adam K.; Angielczyk, Kenneth D.; Ruta, Marcello

2016-04-01

Studies of the effects of mass extinctions on ancient ecosystems have focused on changes in taxic diversity, morphological disparity, abundance, behaviour and resource availability as key determinants of group survival. Crucially, the contribution of life history traits to survival during terrestrial mass extinctions has not been investigated, despite the critical role of such traits for population viability. We use bone microstructure and body size data to investigate the palaeoecological implications of changes in life history strategies in the therapsid forerunners of mammals before and after the Permo-Triassic Mass Extinction (PTME), the most catastrophic crisis in Phanerozoic history. Our results are consistent with truncated development, shortened life expectancies, elevated mortality rates and higher extinction risks amongst post-extinction species. Various simulations of ecological dynamics indicate that an earlier onset of reproduction leading to shortened generation times could explain the persistence of therapsids in the unpredictable, resource-limited Early Triassic environments, and help explain observed body size distributions of some disaster taxa (e.g., Lystrosaurus). Our study accounts for differential survival in mammal ancestors after the PTME and provides a methodological framework for quantifying survival strategies in other vertebrates during major biotic crises.

Indirect evolutionary rescue: prey adapts, predator avoids extinction

PubMed Central

Yamamichi, Masato; Miner, Brooks E

2015-01-01

Recent studies have increasingly recognized evolutionary rescue (adaptive evolution that prevents extinction following environmental change) as an important process in evolutionary biology and conservation science. Researchers have concentrated on single species living in isolation, but populations in nature exist within communities of interacting species, so evolutionary rescue should also be investigated in a multispecies context. We argue that the persistence or extinction of a focal species can be determined solely by evolutionary change in an interacting species. We demonstrate that prey adaptive evolution can prevent predator extinction in two-species predator–prey models, and we derive the conditions under which this indirect evolutionary interaction is essential to prevent extinction following environmental change. A nonevolving predator can be rescued from extinction by adaptive evolution of its prey due to a trade-off for the prey between defense against predation and population growth rate. As prey typically have larger populations and shorter generations than their predators, prey evolution can be rapid and have profound effects on predator population dynamics. We suggest that this process, which we term ‘indirect evolutionary rescue’, has the potential to be critically important to the ecological and evolutionary responses of populations and communities to dramatic environmental change. PMID:26366196

Breeding Young as a Survival Strategy during Earth's Greatest Mass Extinction.

PubMed

Botha-Brink, Jennifer; Codron, Daryl; Huttenlocker, Adam K; Angielczyk, Kenneth D; Ruta, Marcello

2016-04-05

Studies of the effects of mass extinctions on ancient ecosystems have focused on changes in taxic diversity, morphological disparity, abundance, behaviour and resource availability as key determinants of group survival. Crucially, the contribution of life history traits to survival during terrestrial mass extinctions has not been investigated, despite the critical role of such traits for population viability. We use bone microstructure and body size data to investigate the palaeoecological implications of changes in life history strategies in the therapsid forerunners of mammals before and after the Permo-Triassic Mass Extinction (PTME), the most catastrophic crisis in Phanerozoic history. Our results are consistent with truncated development, shortened life expectancies, elevated mortality rates and higher extinction risks amongst post-extinction species. Various simulations of ecological dynamics indicate that an earlier onset of reproduction leading to shortened generation times could explain the persistence of therapsids in the unpredictable, resource-limited Early Triassic environments, and help explain observed body size distributions of some disaster taxa (e.g., Lystrosaurus). Our study accounts for differential survival in mammal ancestors after the PTME and provides a methodological framework for quantifying survival strategies in other vertebrates during major biotic crises.

Rare events in stochastic populations under bursty reproduction

NASA Astrophysics Data System (ADS)

Be'er, Shay; Assaf, Michael

2016-11-01

Recently, a first step was made by the authors towards a systematic investigation of the effect of reaction-step-size noise—uncertainty in the step size of the reaction—on the dynamics of stochastic populations. This was done by investigating the effect of bursty influx on the switching dynamics of stochastic populations. Here we extend this formalism to account for bursty reproduction processes, and improve the accuracy of the formalism to include subleading-order corrections. Bursty reproduction appears in various contexts, where notable examples include bursty viral production from infected cells, and reproduction of mammals involving varying number of offspring. The main question we quantitatively address is how bursty reproduction affects the overall fate of the population. We consider two complementary scenarios: population extinction and population survival; in the former a population gets extinct after maintaining a long-lived metastable state, whereas in the latter a population proliferates despite undergoing a deterministic drift towards extinction. In both models reproduction occurs in bursts, sampled from an arbitrary distribution. Using the WKB approach, we show in the extinction problem that bursty reproduction broadens the quasi-stationary distribution of population sizes in the metastable state, which results in a drastic reduction of the mean time to extinction compared to the non-bursty case. In the survival problem, it is shown that bursty reproduction drastically increases the survival probability of the population. Close to the bifurcation limit our analytical results simplify considerably and are shown to depend solely on the mean and variance of the burst-size distribution. Our formalism is demonstrated on several realistic distributions which all compare well with numerical Monte-Carlo simulations.

Open-path, closed-path and reconstructed aerosol extinction at a rural site.

PubMed

Gordon, Timothy D; Prenni, Anthony J; Renfro, James R; McClure, Ethan; Hicks, Bill; Onasch, Timothy B; Freedman, Andrew; McMeeking, Gavin R; Chen, Ping

2018-04-09

The Handix Scientific Open-Path Cavity Ringdown Spectrometer (OPCRDS) was deployed during summer 2016 in Great Smoky Mountains National Park (GRSM). Extinction coefficients from the relatively new OPCRDS and from a more well-established extinction instrument agreed to within 7%. Aerosol hygroscopic growth (f(RH)) was calculated from the ratio of ambient extinction measured by the OPCRDS to dry extinction measured by a closed-path extinction monitor (Aerodyne's Cavity Attenuated Phase Shift Particulate Matter Extinction Monitor, CAPS PMex). Derived hygroscopicity (RH < 95%) from this campaign agreed with data from 1995 at the same site and time of year, which is noteworthy given the decreasing trend for organics and sulfate in the eastern U.S. However, maximum f(RH) values in 1995 were less than half as large as those recorded in 2016-possibly due to nephelometer truncation losses in 1995. Two hygroscopicity parameterizations were investigated using high time resolution OPCRDS+CAPS PMex data, and the K ext model was more accurate than the γ model. Data from the two ambient optical instruments, the OPCRDS and the open-path nephelometer, generally agreed; however, significant discrepancies between ambient scattering and extinction were observed, apparently driven by a combination of hygroscopic growth effects, which tend to increase nephelometer truncation losses and decrease sensitivity to the wavelength difference between the two instruments as a function of particle size. There was not a statistically significant difference in the mean reconstructed extinction values obtained from the original and the revised IMPROVE (Interagency Monitoring of Protected Visual Environments) equations. On average IMPROVE reconstructed extinction was ~25% lower than extinction measured by the OPCRDS, which suggests that the IMPROVE equations and 24-hr aerosol data are moderately successful in estimating current haze levels at GRSM. However, this conclusion is limited by the coarse temporal resolution and the low dynamic range of the IMPROVE reconstructed extinction.

How interactions between animal movement and landscape processes modify range dynamics and extinction risk

EPA Science Inventory

Range dynamics models now incorporate many of the mechanisms and interactions that drive species distributions. However, connectivity continues to be studied using overly simple distance-based dispersal models with little consideration of how the individual behavior of dispersin...

Competition-Colonization Trade-Offs, Competitive Uncertainty, and the Evolutionary Assembly of Species

PubMed Central

Pillai, Pradeep; Guichard, Frédéric

2012-01-01

We utilize a standard competition-colonization metapopulation model in order to study the evolutionary assembly of species. Based on earlier work showing how models assuming strict competitive hierarchies will likely lead to runaway evolution and self-extinction for all species, we adopt a continuous competition function that allows for levels of uncertainty in the outcome of competition. We then, by extending the standard patch-dynamic metapopulation model in order to include evolutionary dynamics, allow for the coevolution of species into stable communities composed of species with distinct limiting similarities. Runaway evolution towards stochastic extinction then becomes a limiting case controlled by the level of competitive uncertainty. We demonstrate how intermediate competitive uncertainty maximizes the equilibrium species richness as well as maximizes the adaptive radiation and self-assembly of species under adaptive dynamics with mutations of non-negligible size. By reconciling competition-colonization tradeoff theory with co-evolutionary dynamics, our results reveal the importance of intermediate levels of competitive uncertainty for the evolutionary assembly of species. PMID:22448253

Perturbation analysis for patch occupancy dynamics

USGS Publications Warehouse

Martin, Julien; Nichols, James D.; McIntyre, Carol L.; Ferraz, Goncalo; Hines, James E.

2009-01-01

Perturbation analysis is a powerful tool to study population and community dynamics. This article describes expressions for sensitivity metrics reflecting changes in equilibrium occupancy resulting from small changes in the vital rates of patch occupancy dynamics (i.e., probabilities of local patch colonization and extinction). We illustrate our approach with a case study of occupancy dynamics of Golden Eagle (Aquila chrysaetos) nesting territories. Examination of the hypothesis of system equilibrium suggests that the system satisfies equilibrium conditions. Estimates of vital rates obtained using patch occupancy models are used to estimate equilibrium patch occupancy of eagles. We then compute estimates of sensitivity metrics and discuss their implications for eagle population ecology and management. Finally, we discuss the intuition underlying our sensitivity metrics and then provide examples of ecological questions that can be addressed using perturbation analyses. For instance, the sensitivity metrics lead to predictions about the relative importance of local colonization and local extinction probabilities in influencing equilibrium occupancy for rare and common species.

Population dynamics in the presence of quasispecies effects and changing environments

NASA Astrophysics Data System (ADS)

Forster, Robert Burke

2006-12-01

This thesis explores how natural selection acts on organisms such as viruses that have either highly error-prone reproduction or face variable environmental conditions or both. By modeling population dynamics under these conditions, we gain a better understanding of the selective forces at work, both in our simulations and hopefully also in real organisms. With an understanding of the important factors in natural selection we can forecast not only the immediate fate of an existing population but also in what directions such a population might evolve in the future. We demonstrate that the concept of a quasispecies is relevant to evolution in a neutral fitness landscape. Motivated by RNA viruses such as HIV, we use RNA secondary structure as our model system and find that quasispecies effects arise both rapidly and in realistically small populations. We discover that the evolutionary effects of neutral drift, punctuated equilibrium and the selection for mutational robustness extend to the concept of a quasispecies. In our study of periodic environments, we consider the tradeoffs faced by quasispecies in adapting to environmental change. We develop an analytical model to predict whether evolution favors short-term or long-term adaptation and validate our model through simulation. Our results bear directly on the population dynamics of viruses such as West Nile that alternate between two host species. More generally, we discover that a selective pressure exists under these conditions to fuse or split genes with complementary environmental functions. Lastly, we study the general effects of frequency-dependent selection on two strains competing in a periodic environment. Under very general assumptions, we prove that stable coexistence rather than extinction is the likely outcome. The population dynamics of this system may be as simple as stable equilibrium or as complex as deterministic chaos.

IN-SYNC. V. Stellar Kinematics and Dynamics in the Orion A Molecular Cloud

NASA Astrophysics Data System (ADS)

Da Rio, Nicola; Tan, Jonathan C.; Covey, Kevin R.; Cottaar, Michiel; Foster, Jonathan B.; Cullen, Nicholas C.; Tobin, John; Kim, Jinyoung S.; Meyer, Michael R.; Nidever, David L.; Stassun, Keivan G.; Chojnowski, S. Drew; Flaherty, Kevin M.; Majewski, Steven R.; Skrutskie, Michael F.; Zasowski, Gail; Pan, Kaike

2017-08-01

The kinematics and dynamics of young stellar populations enable us to test theories of star formation. With this aim, we continue our analysis of the SDSS-III/APOGEE IN-SYNC survey, a high-resolution near-infrared spectroscopic survey of young clusters. We focus on the Orion A star-forming region, for which IN-SYNC obtained spectra of ˜2700 stars. In Paper IV we used these data to study the young stellar population. Here we study the kinematic properties through radial velocities (v r ). The young stellar population remains kinematically associated with the molecular gas, following a ˜ 10 {km} {{{s}}}-1 gradient along the filament. However, near the center of the region, the v r distribution is slightly blueshifted and asymmetric; we suggest that this population, which is older, is slightly in the foreground. We find evidence for kinematic subclustering, detecting statistically significant groupings of colocated stars with coherent motions. These are mostly in the lower-density regions of the cloud, while the ONC radial velocities are smoothly distributed, consistent with it being an older, more dynamically evolved cluster. The velocity dispersion {σ }v varies along the filament. The ONC appears virialized, or just slightly supervirial, consistent with an old dynamical age. Here there is also some evidence for ongoing expansion, from a v r -extinction correlation. In the southern filament, {σ }v is ˜2-3 times larger than virial in the L1641N region, where we infer a superposition along the line of sight of stellar subpopulations, detached from the gas. In contrast, {σ }v decreases toward L1641S, where the population is again in agreement with a virial state.

Genetic programming for evolving due-date assignment models in job shop environments.

PubMed

Nguyen, Su; Zhang, Mengjie; Johnston, Mark; Tan, Kay Chen

2014-01-01

Due-date assignment plays an important role in scheduling systems and strongly influences the delivery performance of job shops. Because of the stochastic and dynamic nature of job shops, the development of general due-date assignment models (DDAMs) is complicated. In this study, two genetic programming (GP) methods are proposed to evolve DDAMs for job shop environments. The experimental results show that the evolved DDAMs can make more accurate estimates than other existing dynamic DDAMs with promising reusability. In addition, the evolved operation-based DDAMs show better performance than the evolved DDAMs employing aggregate information of jobs and machines.

Transient dynamics of invasive competition: barred owls, spotted owls, habitat, and the demons of competition present.

PubMed

Dugger, Katie M; Anthony, Robert G; Andrews, Lawrence S

2011-10-01

The recent range expansion of Barred Owls (Strix varia) into the Pacific Northwest, where the species now co-occurs with the endemic Northern Spotted Owl (Strix occidentalis caurina), resulted in a unique opportunity to investigate potential competition between two congeneric, previously allopatric species. The primary criticism of early competition research was the use of current species' distribution patterns to infer past processes; however, the recent expansion of the Barred Owl and the ability to model the processes that result in site occupancy (i.e., colonization and extinction) allowed us to address the competitive process directly rather than inferring past processes through current patterns. The purpose of our study was to determine whether Barred Owls had any negative effects on occupancy dynamics of nesting territories by Northern Spotted Owls and how these effects were influenced by habitat characteristics of Spotted Owl territories. We used single-species, multi-season occupancy models and covariates quantifying Barred Owl detections and habitat characteristics to model extinction and colonization rates of Spotted Owl pairs in southern Oregon, USA. We observed a strong, negative association between Barred Owl detections and colonization rates and a strong positive effect of Barred Owl detections on extinction rates of Spotted Owls. We observed increased extinction rates in response to decreased amounts of old forest at the territory core and higher colonization rates when old-forest habitat was less fragmented. Annual site occupancy for pairs reflected the strong effects of Barred Owls on occupancy dynamics with much lower occupancy rates predicted for territories where Barred Owls were detected. The strong Barred Owl and habitat effects on occupancy dynamics of Spotted Owls provided evidence of interference competition between the species. These effects increase the importance of conserving large amounts of contiguous, old-forest habitat to maintain Northern Spotted Owls in the landscape.

Estimation of mussel population response to hydrologic alteration in a southeastern U.S. stream

USGS Publications Warehouse

Peterson, J.T.; Wisniewski, J.M.; Shea, C.P.; Rhett, Jackson C.

2011-01-01

The southeastern United States has experienced severe, recurrent drought, rapid human population growth, and increasing agricultural irrigation during recent decades, resulting in greater demand for the water resources. During the same time period, freshwater mussels (Unioniformes) in the region have experienced substantial population declines. Consequently, there is growing interest in determining how mussel population declines are related to activities associated with water resource development. Determining the causes of mussel population declines requires, in part, an understanding of the factors influencing mussel population dynamics. We developed Pradel reverse-time, tag-recapture models to estimate survival, recruitment, and population growth rates for three federally endangered mussel species in the Apalachicola- Chattahoochee-Flint River Basin, Georgia. The models were parameterized using mussel tag-recapture data collected over five consecutive years from Sawhatchee Creek, located in southwestern Georgia. Model estimates indicated that mussel survival was strongly and negatively related to high flows during the summer, whereas recruitment was strongly and positively related to flows during the spring and summer. Using these models, we simulated mussel population dynamics under historic (1940-1969) and current (1980-2008) flow regimes and under increasing levels of water use to evaluate the relative effectiveness of alternative minimum flow regulations. The simulations indicated that the probability of simulated mussel population extinction was at least 8 times greater under current hydrologic regimes. In addition, simulations of mussel extinction under varying levels of water use indicated that the relative risk of extinction increased with increased water use across a range of minimum flow regulations. The simulation results also indicated that our estimates of the effects of water use on mussel extinction were influenced by the assumptions about the dynamics of the system, highlighting the need for further study of mussel population dynamics. ?? 2011 Springer Science+Business Media, LLC (outside the USA).

Biodiversity, extinctions, and evolution of ecosystems with shared resources

NASA Astrophysics Data System (ADS)

Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno

2017-03-01

We investigate the formation of stable ecological networks where many species share the same resource. We show that such a stable ecosystem naturally occurs as a result of extinctions. We obtain an analytical relation for the number of coexisting species, and we find a relation describing how many species that may become extinct as a result of a sharp environmental change. We introduce a special parameter that is a combination of species traits and resource characteristics used in the model formulation. This parameter describes the pressure on the system to converge, by extinctions. When that stress parameter is large, we obtain that the species traits are concentrated at certain values. This stress parameter is thereby a parameter that determines the level of final biodiversity of the system. Moreover, we show that the dynamics of this limit system can be described by simple differential equations.

Macroecological analyses support an overkill scenario for late Pleistocene extinctions.

PubMed

Diniz-Filho, J A F

2004-08-01

The extinction of megafauna at the end of Pleistocene has been traditionally explained by environmental changes or overexploitation by human hunting (overkill). Despite difficulties in choosing between these alternative (and not mutually exclusive) scenarios, the plausibility of the overkill hypothesis can be established by ecological models of predator-prey interactions. In this paper, I have developed a macroecological model for the overkill hypothesis, in which prey population dynamic parameters, including abundance, geographic extent, and food supply for hunters, were derived from empirical allometric relationships with body mass. The last output correctly predicts the final destiny (survival or extinction) for 73% of the species considered, a value only slightly smaller than those obtained by more complex models based on detailed archaeological and ecological data for each species. This illustrates the high selectivity of Pleistocene extinction in relation to body mass and confers more plausibility on the overkill scenario.

Extinction phase transitions in a model of ecological and evolutionary dynamics

NASA Astrophysics Data System (ADS)

Barghathi, Hatem; Tackkett, Skye; Vojta, Thomas

2017-07-01

We study the non-equilibrium phase transition between survival and extinction of spatially extended biological populations using an agent-based model. We especially focus on the effects of global temporal fluctuations of the environmental conditions, i.e., temporal disorder. Using large-scale Monte-Carlo simulations of up to 3 × 107 organisms and 105 generations, we find the extinction transition in time-independent environments to be in the well-known directed percolation universality class. In contrast, temporal disorder leads to a highly unusual extinction transition characterized by logarithmically slow population decay and enormous fluctuations even for large populations. The simulations provide strong evidence for this transition to be of exotic infinite-noise type, as recently predicted by a renormalization group theory. The transition is accompanied by temporal Griffiths phases featuring a power-law dependence of the life time on the population size.

Short-term predicted extinction of Andean populations of the lizard Stenocercus guentheri (Iguanidae: Tropidurinae).

PubMed

Andrango, María Belén; Sette, Carla; Torres-Carvajal, Omar

2016-12-01

We studied the thermal physiology of the Andean lizard Stenocercus guentheri in order to evaluate the possible effects of global warming on this species. We determined the preferred body temperature (T pref ), critical thermals (CTmin, CTmax), and hours of restriction and activity. T pref was 32.14±1.83°C; CTmin was 8.31°C in adults and 9.14°C in juveniles, whereas CTmax was 43.28°C in adults and 41.68°C in juveniles. To assess extinction risk, we used the model created by Sinervo et al. (2010) and predicted that 16.7% of populations will have a high risk of extinction by 2020, with an increase to 26.7% by 2050. These results suggest that this species, despite being able to maintain its T pref through behavioral thermoregulation and habitat selection, could be physiologically sensitive to climate warming; thus, the potential for local adaptation may be limited under a warmer climate. Further studies focusing on the ability of S. guentheri to evolve higher T pref and thermal tolerances are needed to understand the ability of this species to respond to climate change. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolution of local facilitation in arid ecosystems.

PubMed

Kéfi, Sonia; van Baalen, Minus; Rietkerk, Max; Loreau, Michel

2008-07-01

In harsh environments, sessile organisms can make their habitat more hospitable by buffering environmental stress or increasing resource availability. Although the ecological significance of such local facilitation is widely established, the evolutionary aspects have been seldom investigated. Yet addressing the evolutionary aspects of local facilitation is important because theoretical studies show that systems with such positive interactions can exhibit alternative stable states and that such systems may suddenly become extinct when they evolve (evolutionary suicide). Arid ecosystems currently experience strong changes in climate and human pressures, but little is known about the effects of these changes on the selective pressures exerted on the vegetation. Here, we focus on the evolution of local facilitation in arid ecosystems, using a lattice-structured model explicitly considering local interactions among plants. We found that the evolution of local facilitation depends on the seed dispersal strategy. In systems characterized by short-distance seed dispersal, adaptation to a more stressful environment leads to high local facilitation, allowing the population to escape extinction. In contrast, systems characterized by long-distance seed dispersal become extinct under increased stress even when allowed to adapt. In this case, adaptation in response to climate change and human pressures could give the final push to the desertification of arid ecosystems.

Near-extinction and final burnout in coal combustion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurt, R.H.; Davis, K.A.

The late stages of char combustion have a special technological significance, as carbon conversions of 99% or greater are typically required for the economic operation of pulverized coal fired boilers. In the present article, two independent optical techniques are used to investigate near-extinction and final burnout phenomenas. Captive particle image sequences, combined with in situ optical measurements on entrained particles, provide dramatic illustration of the asymptotic nature of the char burnout process. Single particle combustion to complete burnout is seen to comprise two distinct stages: (1) a rapid high-temperature combustion stage, consuming about 70% of the char carbon and endingmore » with near-extinction of the heterogeneous reactions due to a loss of global particle reactivity, and (2) a final burnout stage occurring slowly at lower temperatures. For particles containing mineral matter, the second stage can be further subdivided into: (2a) late char combustion, which begins after the near-extinction event, and converts carbon-rich particles to mixed particle types at a lower temperature and a slower rate; and (2b) decarburization of ash -- the removal of residual carbon inclusions from inorganic (ash) frameworks in the very late stages of combustion. This latter process can be extremely slow, requiring over an order of magnitude more time than the primary rapid combustion stage. For particles with very little ash, the loss of global reactivity leading to early near-extinction is clearly related to changes in the carbonaceous char matrix, which evolves over the course of combustion. Current global kinetic models used for the prediction of char combustion rates and carbon burnout in boilers do not predict the asymptotic nature of char combustion. More realistic models accounting for the evolution of char structure are needed to make accurate predictions in the range of industrial interest.« less

Climate change, thermal niches, extinction risk and maternal-effect rescue of Toad-headed lizards, Phrynocephalus, in thermal extremes of the Arabian Peninsula to the Tibetan Plateau.

PubMed

Sinervo, Barry; Miles, Donald B; Wu, Yayong; Méndez de la Cruz, Fausto R; Kirchoff, Sebastian; Qi, Yin

2018-02-13

Determining the susceptibility of species to changing thermal niches is a major goal for biologists. In this paper we develop an eco-physiological model of extinction risk under climate change premised on behavioral thermoregulation. Our method downscales operative environmental temperatures, which restrict hours of activity of lizards, h r , for present-day climate (1975) and future climate scenarios (2070). We apply our model using occurrence records of 20 Phrynocephalus lizards (or taxa in species complexes) drawn from literature and museum records. Our analysis is phylogenetically informed, because some clades may be more sensitive to rising temperatures. Computed h r limits predict local extirpations among Phrynocephalus lizards at continental scales and delineate upper boundaries of thermal niches as defined by Extreme Value Distributions. Under the 8.5 Representative Concentration Pathway scenario, we predict extirpation of 64% of local populations by 2070 across 20 Phrynocephalus species, and 12 are at high risk of total extinction due to thermal limits being exceeded. In tandem with global strategies of lower CO 2 emissions, we propose regional strategies for establishing new National Parks to protect extinction-prone taxa by preserving high-elevation climate refugia within existing sites of species occurrence. We propose that evolved acclimatization - maternal plasticity - may ameliorate risk, but is poorly studied. Previous studies revealed that adaptive maternal plasticity by thermoregulating gravid females alter progeny thermal preferences by ±1°C. We describe plasticity studies for extinction-prone species that could assess whether they might be buffered from climate warming - a self-rescue. We discuss an epigenetic framework for studying such maternal-effect evolution. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A model for the emergence of cooperation, interdependence, and structure in evolving networks.

PubMed

Jain, S; Krishna, S

2001-01-16

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent "catalytic" and "inhibitory" interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set, appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the autocatalytic set enlarges and percolates through the network in a short analytically determined timescale. This self organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long timescales triggered by the chance elimination of "keystone" species, followed by recoveries.

A model for the emergence of cooperation, interdependence, and structure in evolving networks

NASA Astrophysics Data System (ADS)

Jain, Sanjay; Krishna, Sandeep

2001-01-01

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent "catalytic" and "inhibitory" interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set, appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the autocatalytic set enlarges and percolates through the network in a short analytically determined timescale. This self organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long timescales triggered by the chance elimination of "keystone" species, followed by recoveries.

Intermediate disturbance in experimental landscapes improves persistence of beetle metapopulations.

PubMed

Govindan, Byju N; Feng, Zhilan; DeWoody, Yssa D; Swihart, Robert K

2015-03-01

Human-dominated landscapes often feature patches that fluctuate in suitability through space and time, but there is little experimental evidence relating the consequences of dynamic patches for species persistence. We used a spatially and temporally dynamic metapopulation model to assess and compare metapopulation capacity and persistence for red flour beetles (Tribolium castaneum) in experimental landscapes differentiated by resource structure, patch dynamics (destruction and restoration), and connectivity. High connectivity increased the colonization rate of beetles, but this effect was less pronounced in heterogeneous relative to homogeneous landscapes. Higher connectivity and faster patch dynamics increased extinction rates in landscapes. Lower connectivity promoted density-dependent emigration. Heterogeneous landscapes containing patches of different carrying capacity enhanced landscape-level occupancy probability. The highest metapopulation capacity and persistence was observed in landscapes with heterogeneous patches, low connectivity, and slow patch dynamics. Control landscapes with no patch dynamics exhibited rapid declines in abundance and approached extinction due to increased adult mortality in the matrix, higher pupal cannibalism by adults, and extremely low rates of exchange between remaining habitable patches. Our results highlight the role of intermediate patch dynamics, intermediate connectivity, and the nature of density dependence of emigration for persistence of species in heterogeneous landscapes. Our results also demonstrate the importance of incorporating local dynamics into the estimation of metapopulation capacity for conservation planning.

Determinants of extinction-colonization dynamics in Mediterranean butterflies: the role of landscape, climate and local habitat features.

PubMed

Fernández-Chacón, Albert; Stefanescu, Constantí; Genovart, Meritxell; Nichols, James D; Hines, James E; Páramo, Ferran; Turco, Marco; Oro, Daniel

2014-01-01

Many species are found today in the form of fragmented populations occupying patches of remnant habitat in human-altered landscapes. The persistence of these population networks requires a balance between extinction and colonization events assumed to be primarily related to patch area and isolation, but the contribution of factors such as the characteristics of patch and matrix habitats, the species' traits (habitat specialization and dispersal capabilities) and variation in climatic conditions have seldom been evaluated simultaneously. The identification of environmental variables associated with patch occupancy and turnover may be especially useful to enhance the persistence of multiple species under current global change. However, for robust inference on occupancy and related parameters, we must account for detection errors, a commonly overlooked problem that leads to biased estimates and misleading conclusions about population dynamics. Here, we provide direct empirical evidence of the effects of different environmental variables on the extinction and colonization rates of a rich butterfly community in the western Mediterranean. The analysis was based on a 17-year data set containing detection/nondetection data on 73 butterfly species for 26 sites in north-eastern Spain. Using multiseason occupancy models, which take into account species' detectability, we were able to obtain robust estimates of local extinction and colonization probabilities for each species and test the potential effects of site covariates such as the area of suitable habitat, topographic variability, landscape permeability around the site and climatic variability in aridity conditions. Results revealed a general pattern across species with local habitat composition and landscape features as stronger predictors of occupancy dynamics compared with topography and local aridity. Increasing area of suitable habitat in a site strongly decreased local extinction risks and, for a number of species, both higher amounts of suitable habitat and more permeable landscapes increased colonization rates. Nevertheless, increased topographic variability decreased the extinction risk of bad dispersers, a group of species with significantly lower colonization rates. Our models predicted higher sensitivity of the butterfly assemblages to deterministic changes in habitat features rather than to stochastic weather patterns, with some relationships being clearly dependent on the species' traits. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Musculoskeletal modelling of an ostrich (Struthio camelus) pelvic limb: influence of limb orientation on muscular capacity during locomotion

PubMed Central

Rankin, Jeffery W.; Rubenson, Jonas; Rosenbluth, Kate H.; Siston, Robert A.; Delp, Scott L.

2015-01-01

We developed a three-dimensional, biomechanical computer model of the 36 major pelvic limb muscle groups in an ostrich (Struthio camelus) to investigate muscle function in this, the largest of extant birds and model organism for many studies of locomotor mechanics, body size, anatomy and evolution. Combined with experimental data, we use this model to test two main hypotheses. We first query whether ostriches use limb orientations (joint angles) that optimize the moment-generating capacities of their muscles during walking or running. Next, we test whether ostriches use limb orientations at mid-stance that keep their extensor muscles near maximal, and flexor muscles near minimal, moment arms. Our two hypotheses relate to the control priorities that a large bipedal animal might evolve under biomechanical constraints to achieve more effective static weight support. We find that ostriches do not use limb orientations to optimize the moment-generating capacities or moment arms of their muscles. We infer that dynamic properties of muscles or tendons might be better candidates for locomotor optimization. Regardless, general principles explaining why species choose particular joint orientations during locomotion are lacking, raising the question of whether such general principles exist or if clades evolve different patterns (e.g., weighting of muscle force–length or force–velocity properties in selecting postures). This leaves theoretical studies of muscle moment arms estimated for extinct animals at an impasse until studies of extant taxa answer these questions. Finally, we compare our model’s results against those of two prior studies of ostrich limb muscle moment arms, finding general agreement for many muscles. Some flexor and extensor muscles exhibit self-stabilization patterns (posture-dependent switches between flexor/extensor action) that ostriches may use to coordinate their locomotion. However, some conspicuous areas of disagreement in our results illustrate some cautionary principles. Importantly, tendon-travel empirical measurements of muscle moment arms must be carefully designed to preserve 3D muscle geometry lest their accuracy suffer relative to that of anatomically realistic models. The dearth of accurate experimental measurements of 3D moment arms of muscles in birds leaves uncertainty regarding the relative accuracy of different modelling or experimental datasets such as in ostriches. Our model, however, provides a comprehensive set of 3D estimates of muscle actions in ostriches for the first time, emphasizing that avian limb mechanics are highly three-dimensional and complex, and how no muscles act purely in the sagittal plane. A comparative synthesis of experiments and models such as ours could provide powerful synthesis into how anatomy, mechanics and control interact during locomotion and how these interactions evolve. Such a framework could remove obstacles impeding the analysis of muscle function in extinct taxa. PMID:26082859

Synthesis of Copper–Silica Core–Shell Nanostructures with Sharp and Stable Localized Surface Plasmon Resonance

DOE PAGES

Crane, Cameron C.; Wang, Feng; Li, Jun; ...

2017-02-21

Copper nanoparticles exhibit intense and sharp localized surface plasmon resonance (LSPR) in the visible region; however, the LSPR peaks become weak and broad when exposed to air due to the oxidation of Cu. In this work, the Cu nanoparticles are successfully encapsulated in SiO 2 by employing trioctyl-n-phosphine (TOP)-capped Cu nanoparticles for the sol–gel reaction, yielding an aqueous Cu–SiO 2 core–shell suspension with stable and well-preserved LSPR properties of the Cu cores. With the TOP capping, the oxidation of the Cu cores in the microemulsion was significantly reduced, thus allowing the Cu cores to sustain the sol–gel process used formore » coating the SiO 2 protection layer. It was found that the self-assembled TOP-capped Cu nanoparticles were spontaneously disassembled during the sol–gel reaction, thus recovering the LSPR of individual particles. During the disassembling progress, the extinction spectrum of the nanocube agglomerates evolved from a broad extinction profile to a narrow and sharp peak. For a mixture of nanocubes and nanorods, the spectra evolved to two distinct peaks during the dissembling process. The observed spectra match well with the numerical simulations. In conclusion, these Cu–SiO 2 core–shell nanoparticles with sharp and stable LSPR may greatly expand the utilization of Cu nanoparticles in aqueous environments.« less

Epoch-based likelihood models reveal no evidence for accelerated evolution of viviparity in squamate reptiles in response to cenozoic climate change.

PubMed

King, Benedict; Lee, Michael S Y

2015-09-01

A broad scale analysis of the evolution of viviparity across nearly 4,000 species of squamates revealed that origins increase in frequency toward the present, raising the question of whether rates of change have accelerated. We here use simulations to show that the increased frequency is within the range expected given that the number of squamate lineages also increases with time. Novel, epoch-based methods implemented in BEAST (which allow rates of discrete character evolution to vary across time-slices) also give congruent results, with recent epochs having very similar rates to older epochs. Thus, contrary to expectations, there was no accelerated burst of origins of viviparity in response to global cooling during the Cenozoic or glacial cycles during the Plio-Pleistocene. However, if one accepts the conventional view that viviparity is more likely to evolve than to be lost, and also the evidence here that viviparity has evolved with similar regularity throughout the last 200 Ma, then the absence of large, ancient clades of viviparous squamates (analogs to therian mammals) requires explanation. Viviparous squamate lineages might be more prone to extinction than are oviparous lineages, due to their prevalance at high elevations and latitudes and thus greater susceptibility to climate fluctuations. If so, the directional bias in character evolution would be offset by the bias in extinction rates. © 2015 Wiley Periodicals, Inc.

Synthesis of Copper–Silica Core–Shell Nanostructures with Sharp and Stable Localized Surface Plasmon Resonance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crane, Cameron C.; Wang, Feng; Li, Jun

Copper nanoparticles exhibit intense and sharp localized surface plasmon resonance (LSPR) in the visible region; however, the LSPR peaks become weak and broad when exposed to air due to the oxidation of Cu. In this work, the Cu nanoparticles are successfully encapsulated in SiO 2 by employing trioctyl-n-phosphine (TOP)-capped Cu nanoparticles for the sol–gel reaction, yielding an aqueous Cu–SiO 2 core–shell suspension with stable and well-preserved LSPR properties of the Cu cores. With the TOP capping, the oxidation of the Cu cores in the microemulsion was significantly reduced, thus allowing the Cu cores to sustain the sol–gel process used formore » coating the SiO 2 protection layer. It was found that the self-assembled TOP-capped Cu nanoparticles were spontaneously disassembled during the sol–gel reaction, thus recovering the LSPR of individual particles. During the disassembling progress, the extinction spectrum of the nanocube agglomerates evolved from a broad extinction profile to a narrow and sharp peak. For a mixture of nanocubes and nanorods, the spectra evolved to two distinct peaks during the dissembling process. The observed spectra match well with the numerical simulations. In conclusion, these Cu–SiO 2 core–shell nanoparticles with sharp and stable LSPR may greatly expand the utilization of Cu nanoparticles in aqueous environments.« less

Dynamic expression of FKBP5 in the medial prefrontal cortex regulates resiliency to conditioned fear

PubMed Central

Criado-Marrero, Marangelie; Morales Silva, Roberto J.; Velazquez, Bethzaly; Hernández, Anixa; Colon, María; Cruz, Emmanuel; Soler-Cedeño, Omar; Porter, James T.

2017-01-01

The factors influencing resiliency to the development of post-traumatic stress disorder (PTSD) remain to be elucidated. Clinical studies associate PTSD with polymorphisms of the FK506 binding protein 5 (FKBP5). However, it is unclear whether changes in FKBP5 expression alone could produce resiliency or susceptibility to PTSD-like symptoms. In this study, we used rats as an animal model to examine whether FKBP5 in the infralimbic (IL) or prelimbic (PL) medial prefrontal cortex regulates fear conditioning or extinction. First, we examined FKBP5 expression in IL and PL during fear conditioning or extinction. In contrast to the stable expression of FKBP5 seen in PL, FKBP5 expression in IL increased after fear conditioning and remained elevated even after extinction suggesting that IL FKBP5 levels may modulate fear conditioning or extinction. Consistent with this possibility, reducing basal FKBP5 expression via local infusion of FKBP5–shRNA into IL reduced fear conditioning. Furthermore, reducing IL FKBP5, after consolidation of the fear memory, enhanced extinction memory indicating that IL FKBP5 opposed formation of the extinction memory. Our findings demonstrate that lowering FKBP5 expression in IL is sufficient to both reduce fear acquisition and enhance extinction, and suggest that lower expression of FKBP5 in the ventral medial prefrontal cortex could contribute to resiliency to PTSD. PMID:28298552

Adaptive evolution of body size subject to indirect effect in trophic cascade system.

PubMed

Wang, Xin; Fan, Meng; Hao, Lina

2017-09-01

Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model. First, an eco-evolutionary model incorporating the rapid evolution is formulated to investigate the effect of rapid evolution of the consumer's body size, and to explore the impact of density-mediate indirect effect on the population dynamics and trait dynamics. Next, by employing the adaptive dynamic theory, a long-term evolutionary model of consumer body size is formulated to evaluate the effect of long-term evolution on the population dynamics and the effect of trait-mediate indirect effect. Those models admit rich dynamics that has not been observed yet in empirical studies. It is found that, both in the trait-mediated and density-mediated system, the body size of consumer in predator-consumer-resource interaction (indirect effect) evolves smaller than that in consumer-resource and predator-consumer interaction (direct effect). Moreover, in the density-mediated system, we found that the evolution of consumer body size contributes to avoiding consumer extinction (i.e., evolutionary rescue). The trait-mediate and density-mediate effects may produce opposite evolutionary response. This study suggests that the trophic cascade indirect effect affects consumer evolution, highlights a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. The modeling approaches provide avenue for study on indirect effects from an evolutionary perspective. Copyright © 2017 Elsevier B.V. All rights reserved.

Assessing Regional and Interspecific Variation in Threshold Responses of Forest Breeding Birds through Broad Scale Analyses

PubMed Central

van der Hoek, Yntze; Renfrew, Rosalind; Manne, Lisa L.

2013-01-01

Background Identifying persistence and extinction thresholds in species-habitat relationships is a major focal point of ecological research and conservation. However, one major concern regarding the incorporation of threshold analyses in conservation is the lack of knowledge on the generality and transferability of results across species and regions. We present a multi-region, multi-species approach of modeling threshold responses, which we use to investigate whether threshold effects are similar across species and regions. Methodology/Principal Findings We modeled local persistence and extinction dynamics of 25 forest-associated breeding birds based on detection/non-detection data, which were derived from repeated breeding bird atlases for the state of Vermont. We did not find threshold responses to be particularly well-supported, with 9 species supporting extinction thresholds and 5 supporting persistence thresholds. This contrasts with a previous study based on breeding bird atlas data from adjacent New York State, which showed that most species support persistence and extinction threshold models (15 and 22 of 25 study species respectively). In addition, species that supported a threshold model in both states had associated average threshold estimates of 61.41% (SE = 6.11, persistence) and 66.45% (SE = 9.15, extinction) in New York, compared to 51.08% (SE = 10.60, persistence) and 73.67% (SE = 5.70, extinction) in Vermont. Across species, thresholds were found at 19.45–87.96% forest cover for persistence and 50.82–91.02% for extinction dynamics. Conclusions/Significance Through an approach that allows for broad-scale comparisons of threshold responses, we show that species vary in their threshold responses with regard to habitat amount, and that differences between even nearby regions can be pronounced. We present both ecological and methodological factors that may contribute to the different model results, but propose that regardless of the reasons behind these differences, our results merit a warning that threshold values cannot simply be transferred across regions or interpreted as clear-cut targets for ecosystem management and conservation. PMID:23409106

Critical edge between frozen extinction and chaotic life

NASA Astrophysics Data System (ADS)

Monetti, Roberto A.; Albano, Ezequiel V.

1995-12-01

The cellular automata ``game of life'' (GL) proposed by J. Conway simulates the dynamic evolution of a society of living organisms. It has been extensively studied in order to understand the emergence of complexity and diversity from a set of local rules. More recently, the capability of GL to self-oranize into a critical state has opened an interesting debate. In this work we adopt a different approach: by introducing stochastic rules in the GL it is found that ``life'' exhibits a very rich critical behavior. Discontinuous (first-order) irreversible phase transitions (IPT's) between an extinct phase and a steady state supporting life are found. A precise location of the critical edge is achieved by means of an epidemic analysis, which also allows us to determine dynamic critical exponents. Furthermore, by means of a damage spreading study we conclude that the living phase is chaotic. The edge of the frozen-chaotic transition coincides with that of the IPT's life extinction. Close to the edge, fractal spreading of the damage is observed; however, deep inside the living phase such spreading becomes homogeneous. (c) 1995 The American Physical Society

Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene.

PubMed

Crees, Jennifer J; Carbone, Chris; Sommer, Robert S; Benecke, Norbert; Turvey, Samuel T

2016-03-30

The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18,700 mammalian zooarchaeological records for the last 11,700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of 'static' past baselines to inform current-day environmental management and restoration. © 2016 The Author(s).

Time-dependent extinction rate and species abundance in a tangled-nature model of biological evolution.

PubMed

Hall, Matt; Christensen, Kim; di Collobiano, Simone A; Jensen, Henrik Jeldtoft

2002-07-01

We present a model of evolutionary ecology consisting of a web of interacting individuals, a tangle-nature model. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and the macroevolutionary mode of the dynamics are emergent properties. The macrodynamics exhibit intermittent two-mode switching with a gradually decreasing extinction rate. The generated ecologies become gradually better adapted as well as more complex in a collective sense. The form of the species abundance curve compares well with observed functional forms. The model's error threshold can be understood in terms of the characteristics of the two dynamical modes of the system.

Geographic range size and extinction risk assessment in nomadic species.

PubMed

Runge, Claire A; Tulloch, Ayesha; Hammill, Edd; Possingham, Hugh P; Fuller, Richard A

2015-06-01

Geographic range size is often conceptualized as a fixed attribute of a species and treated as such for the purposes of quantification of extinction risk; species occupying smaller geographic ranges are assumed to have a higher risk of extinction, all else being equal. However many species are mobile, and their movements range from relatively predictable to-and-fro migrations to complex irregular movements shown by nomadic species. These movements can lead to substantial temporary expansion and contraction of geographic ranges, potentially to levels which may pose an extinction risk. By linking occurrence data with environmental conditions at the time of observations of nomadic species, we modeled the dynamic distributions of 43 arid-zone nomadic bird species across the Australian continent for each month over 11 years and calculated minimum range size and extent of fluctuation in geographic range size from these models. There was enormous variability in predicted spatial distribution over time; 10 species varied in estimated geographic range size by more than an order of magnitude, and 2 species varied by >2 orders of magnitude. During times of poor environmental conditions, several species not currently classified as globally threatened contracted their ranges to very small areas, despite their normally large geographic range size. This finding raises questions about the adequacy of conventional assessments of extinction risk based on static geographic range size (e.g., IUCN Red Listing). Climate change is predicted to affect the pattern of resource fluctuations across much of the southern hemisphere, where nomadism is the dominant form of animal movement, so it is critical we begin to understand the consequences of this for accurate threat assessment of nomadic species. Our approach provides a tool for discovering spatial dynamics in highly mobile species and can be used to unlock valuable information for improved extinction risk assessment and conservation planning. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

Occupancy dynamics in human-modified landscapes in a tropical island: implications for conservation design

USGS Publications Warehouse

Irizarry, Julissa I.; Collazo, Jaime A.; Dinsmore, Stephen J.

2016-01-01

AimAvian communities in human-modified landscapes exhibit varying patterns of local colonization and extinction rates, determinants of species occurrence. Our objective was to model these processes to identify habitat features that might enable movements and account for occupancy patterns in habitat matrices between the Guanica and Susua forest reserves. This knowledge is central to conservation design, particularly in ever changing insular landscapes.LocationSouth-western Puerto Rico.MethodsWe used a multiseason occupancy modelling approach to quantify seasonal estimates of occupancy, and colonization and extinction rates of seven resident avian species surveyed over five seasons from January 2010 to June 2011. We modelled parameters by matrix type, expressions of survey station isolation, quality, amount of forest cover and context (embedded in forest patch).ResultsSeasonal occupancy remained stable throughout the study for all species, consistent with seasonally constant colonization and extinction probabilities. Occupancy was mediated by matrix type, higher in reserves and forested matrix than in the urban and agricultural matrices. This pattern is in accord with the forest affinities of all but an open-habitat specialist. Puerto Rican Spindalis (Spindalis portoricensis) exhibited high occupancy in the urban matrix, highlighting the adaptability of some insular species to novel environments. Highest colonization rates occurred when perching structures were at ≤ 500 m. Survey stations with at least three fruiting tree species and 61% forest cover exhibited lowest seasonal extinction rates.Main conclusionsOur work identified habitat features that influenced seasonal probabilities of colonization and extinction in a human-modified landscape. Conservation design decisions are better informed with increased knowledge about interpatch distances to improve matrix permeability, and habitat features that increase persistence or continued use of habitat stepping stones. A focus on dynamic processes is valuable because conservation actions directly influence colonization and extinction rates, and thus, a quantitative means to gauge their benefit.

Boron isotopes in brachiopods during the end-Permian mass extinction: constraints on pH evolution and seawater chemistry

NASA Astrophysics Data System (ADS)

Jurikova, Hana; Gutjahr, Marcus; Liebetrau, Volker; Brand, Uwe; Posenato, Renato; Garbelli, Claudio; Angiolini, Lucia; Eisenhauer, Anton

2017-04-01

The global biogeochemical cycling of carbon is fundamental for life on Earth with the ocean playing a key role as the largest and dynamically evolving CO2 reservoir. The boron isotope composition (commonly expressed in δ11B) of marine calcium carbonate is considered to be one of the most reliable paleo-pH proxies, potentially enabling us to reconstruct past ocean pH changes and understand carbon cycle perturbations along Earth's geological record (e.g. Foster et al., 2008; Clarkson et al., 2015). Brachiopods present an advantageous and largely underutilised archive for Phanerozoic carbon cycle reconstructions considering their high abundance in the geological record and its origin dating back to the early Cambrian. Moreover, their shell made of low-magnesium calcite makes these marine calcifiers more resistant to post-depositional diagenetic alteration of primary chemical signals. We have investigated the δ11B using MC-ICP-MS (Neptune Plus) and B/Ca and other elemental ratios (Mg/Ca, Sr/Ca, Al/Ca, Li/Ca, Ba/Ca, Na/Ca and Fe/Ca) using ICP-MS-Quadrupole (Agilent 7500cx) from the same specimens in pristine brachiopod shells from two sections from northern Italy during the Late Permian. These sections cover the δ13C excursion in excess of ˜4 ‰ (Brand et al., 2012) and are associated with major climate and environmental perturbations that lead to the mass extinction event at the Permian-Triassic boundary. Particular emphasis will be placed on the implications of our new paleo-pH estimates on the seawater chemistry during the Late Permian. Brand, U., Posenato, R., Came, R., Affek, H., Angiolini, L., Azmy, K. and Farabegoli, E.: The end-Permian mass extinction: A rapid volcanic CO2 and CH4-climatic catastrophe, Chemical Geology 323, 121-144, doi:10.1016/j.chemgeo.2012.06.015, 2012. Clarkson, M.O., Kasemann, S.A., Wood, R.A., Lenton, T.M., Daines, S.J., Richoz, S., Ohnemueller, F., Meixner, A., Poulton, S.W. and Tipper, E.T.: Ocean acidification and the Permo-Triassic mass extinction. Science 348, 229-232, doi: 10.1126/science.aaa0193, 2015. Foster, G.L.: Seawater pH, pCO2 and [CO32-] variations in the Caribbean Sea over the last 130 kyr: A boron isotope and B/Ca study of planktic foraminifera. Earth and Planetary Science Letters 271, 254-266. doi:10.1016/j.epsl.2008.04.015, 2008.

Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats.

PubMed

Han, Pu; Deem, Michael W

2017-02-01

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria coevolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the re-entrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon. © 2017 The Author(s).

Did the Ancient Crenarchaeal Viruses from the Dawn of Life Survive Exceptionally Well the Eons of Meteorite Bombardment?

NASA Astrophysics Data System (ADS)

Jalasvuori, Matti; Bamford, Jaana K. H.

2009-02-01

The viruses of Crenarchaeota are unexpectedly diverse in their morphologies, and most have no, or few, genes related to bacterial, eukaryal, euryarchaeal, or other crenarchaeal viruses. Though several different virus morphotypes have been discovered in enrichment cultures of microbial communities collected from geothermally heated environments around the world, the origins of such differences are unknown. We present a model that combines consideration of Earth's geological history, the early emergence of hyperthermophiles, and the early formation of viruses from primordial genes with the intent to explain this vast diversity of crenarchaeal viruses. Several meteorite- or flood basalt-induced extinction events in the past resulted in a reduction in the numbers of cellular organisms. Acidophilic hyperthermophiles survived the global thermal rises and, therefore, still host a wide variety of ancient virus morphotypes. In contrast, other, more "recent" cellular lineages have lost the majority of their original viruses, as they have been separated geologically and genetically, and have gone through several near-extinction-level episodes of decimation. This view suggests that, among crenarchaeal viruses, the direct descendants of very early genetic elements are well preserved; thus, their examination would improve our understanding as to how life actually evolved from its origins to the complex cellular systems we see today. We also present a hypothesis that describes the role of viral armadas and extinctions during evolution, as extinctions may have episodically eliminated most of the abusive parasites.

Lidar Observations of Tropospheric Aerosols Over Northeastern South Africa During the ARREX and SAFARI-2000 Dry Season Experiments

NASA Technical Reports Server (NTRS)

Campbell, James R.; Welton, Ellsworth J.; Spinhirne, James D.; Ji, Qiang; Tsay, Si-Chee; Piketh, Stuart J.; Barenbrug, Marguerite; Holben, Brent; Starr, David OC. (Technical Monitor)

2002-01-01

During the ARREX-1999 and SAFARI-2000 Dry Season experiments a micropulse lidar (523 nm) instrument was operated at the Skukuza Airport in northeastern South Africa. The Mar was collocated with a diverse array of passive radiometric equipment. For SAFARI-2000 the processed Mar data yields a daytime time-series of layer mean/derived aerosol optical properties, including extinction-to-backscatter ratios and vertical extinction cross-section profile. Combined with 523 run aerosol optical depth and spectral Angstrom exponent calculations from available CIMEL sun-photometer data and normalized broadband flux measurements the temporal evolution of the near surface aerosol layer optical properties is analyzed for climatological trends. For the densest smoke/haze events the extinction-to-backscatter ratio is found to be between 60-80/sr, and corresponding Angstrom exponent calculations near and above 1.75. The optical characteristics of an evolving smoke event from SAFARI-2000 are extensively detailed. The advecting smoke was embedded within two distinct stratified thermodynamic layers, causing the particulate mass to advect over the instrument array in an incoherent manner on the afternoon of its occurrence. Surface broadband flux forcing due to the smoke is calculated, as is the evolution in the vertical aerosol extinction profile as measured by the Han Finally, observations of persistent elevated aerosol during ARREX-1999 are presented and discussed. The lack of corroborating observations the following year makes these observation; both unique and noteworthy in the scope of regional aerosol transport over southern Africa.

Worrying affects associative fear learning: a startle fear conditioning study.

PubMed

Gazendam, Femke J; Kindt, Merel

2012-01-01

A valuable experimental model for the pathogenesis of anxiety disorders is that they originate from a learned association between an intrinsically non-aversive event (Conditioned Stimulus, CS) and an anticipated disaster (Unconditioned Stimulus, UCS). Most anxiety disorders, however, do not evolve from a traumatic experience. Insights from neuroscience show that memory can be modified post-learning, which may elucidate how pathological fear can develop after relatively mild aversive events. Worrying--a process frequently observed in anxiety disorders--is a potential candidate to strengthen the formation of fear memory after learning. Here we tested in a discriminative fear conditioning procedure whether worry strengthens associative fear memory. Participants were randomly assigned to either a Worry (n = 23) or Control condition (n = 25). After fear acquisition, the participants in the Worry condition processed six worrisome questions regarding the personal aversive consequences of an electric stimulus (UCS), whereas the Control condition received difficult but neutral questions. Subsequently, extinction, reinstatement and re-extinction of fear were tested. Conditioned responding was measured by fear-potentiated startle (FPS), skin conductance (SCR) and UCS expectancy ratings. Our main results demonstrate that worrying resulted in increased fear responses (FPS) to both the feared stimulus (CS(+)) and the originally safe stimulus (CS(-)), whereas FPS remained unchanged in the Control condition. In addition, worrying impaired both extinction and re-extinction learning of UCS expectancy. The implication of our findings is that they show how worry may contribute to the development of anxiety disorders by affecting associative fear learning.

Maximisation Principles in Foodwebs and Daisyworlds

NASA Astrophysics Data System (ADS)

Ackland, G. J.; Gallagher, I. D.

2005-12-01

Using computer simulation we investigate whether the steady-state time averaged state of a self-organising system with many internal degrees of freedom can be described by optimising a single quantity. Our open systems follow evolutionary dynamics hence the conservation laws and energy-based state probabilities which underpin Hamiltonian dynamics do not apply. We find that these dynamics observe a novel optimality principle, that the system self-organises to a state which maximises the sustainable amount of replicating objects. We have studied a number of mathematical models of evolving replicating systems: daisyworlds[1], logistic map and generalized Lotka Volterra foodwebs[2]. Each is characterised by being (1) "open" - resources flow into and out of the system. (2) "self-regulating" - the inflow/outflow of resources is not fixed externally. (3) "evolving" - the increase in population at the next timestep depends on the population at the current timestep. These properties violate the assumptions made in deriving optimality principles such as free energy minimisation, maximum/mimimum entropy production etc., so it is unsurprising that they are not observed. The absence of a Hamiltonian for ecosystems is particularly problematic for coupled models of life and the environment - moreover there is ambiguity in defining an entropy for an ecosystem. By considering large and small species within the 2D daisyworld model we show that the appropriate measure comes from the interaction with the rest of the system, not the information theoretic entropy of the daisy field. We introduce evolution within the classic Lotka-Volterra model for interaction between species in an ecosystem. Generalisation to many species is straightforward, but the resulting network is usually unstable. By restricting the number of links between species it is possible to form a stable network by evolution - allowing some species to go extinct. This method can be used to generate arbitrarily large network, from which a treelike structure of trophic levels emerges, but typically the number of connection is much smaller than in real ecosystems. Here, we show that applying evolution to the strength of the links, rather than simply their existence, stabilises the entire network and generates a power-law distribution of link strengths. The network dynamics are chaotic, but as a whole tend towards maximising the use of resources. If the dynamics are linearised to remove the chaos, the scale-free link strengths also disappear. [1] Maximisation Principles and Daisyworld G.J. Ackland J.Theo.Bio. 227, 121, (2004) [2] Stabilization of large generalized Lotka-Volterra foodwebs by evolutionary feedback G.J. Ackland and I.D. Gallagher Phys Rev Lett 93 158701 2004

Use of dynamic occupancy models to assess the response of Darters (Teleostei: Percidae) to varying hydrothermal conditions in a southeastern United States tailwater

USGS Publications Warehouse

Shea, C.P.; Bettoli, Phillip William; Potoka, K. M.; Saylor, C. F.; Shute, P. W.

2015-01-01

During the past 100 years, most large rivers in North America have been altered for flood control, hydropower, navigation or water supply development. Although these activities clearly provide important human services, their associated environmental disturbances can profoundly affect stream-dwelling organisms. We used dynamic multi-species occupancy models combined with a trait-based approach to estimate the influence of site-level and species-level characteristics on patch dynamic rates for 15 darter species native to the Elk River, a large, flow-regulated Tennessee River tributary in Tennessee and Alabama. Dynamic occupancy modelling results indicated that for every 2.5 °C increase in stream temperature, darters were 3.94 times more likely to colonize previously unoccupied stream reaches. Additionally, large-bodied darter species were 3.72 times more likely to colonize stream reaches compared with small-bodied species, but crevice-spawning darter species were 5.24 times less likely to colonize previously unoccupied stream reaches. In contrast, darters were 2.21 times less likely to become locally extinct for every 2.5 °C increase in stream temperature, but high stream discharge conditions elevated the risk of local extinction. Lastly, the presence of populations in neighbouring upstream study reaches contributed to a lower risk of extinction, whereas the presence of populations in neighbouring downstream study reaches contributed to higher rates of colonization. Our study demonstrates the application of a trait-based approach combined with a metapopulation framework to assess the patch dynamics of darters in a regulated river. Results from our study will provide a baseline for evaluating the ecological consequences of alternative dam operations.

Evolutionary origins and diversification of proteobacterial mutualists.

PubMed

Sachs, Joel L; Skophammer, Ryan G; Bansal, Nidhanjali; Stajich, Jason E

2014-01-22

Mutualistic bacteria infect most eukaryotic species in nearly every biome. Nonetheless, two dilemmas remain unresolved about bacterial-eukaryote mutualisms: how do mutualist phenotypes originate in bacterial lineages and to what degree do mutualists traits drive or hinder bacterial diversification? Here, we reconstructed the phylogeny of the hyperdiverse phylum Proteobacteria to investigate the origins and evolutionary diversification of mutualistic bacterial phenotypes. Our ancestral state reconstructions (ASRs) inferred a range of 34-39 independent origins of mutualist phenotypes in Proteobacteria, revealing the surprising frequency with which host-beneficial traits have evolved in this phylum. We found proteobacterial mutualists to be more often derived from parasitic than from free-living ancestors, consistent with the untested paradigm that bacterial mutualists most often evolve from pathogens. Strikingly, we inferred that mutualists exhibit a negative net diversification rate (speciation minus extinction), which suggests that mutualism evolves primarily via transitions from other states rather than diversification within mutualist taxa. Moreover, our ASRs infer that proteobacterial mutualist lineages exhibit a paucity of reversals to parasitism or to free-living status. This evolutionary conservatism of mutualism is contrary to long-standing theory, which predicts that selection should often favour mutants in microbial mutualist populations that exploit or abandon more slowly evolving eukaryotic hosts.

Stable isotope ecology of Miocene bovids from Northern Greece and the ape/monkey turnover in the Balkans.

PubMed

Merceron, Gildas; Kostopoulos, Dimitris S; Bonis, Louis de; Fourel, François; Koufos, George D; Lécuyer, Christophe; Martineau, François

2013-08-01

Eurasia was home to a great radiation of hominoid primates during the Miocene. All were extinct by the end of the Miocene in Western Eurasia. Here, we investigate the hypothesis of climate and vegetation changes at a local scale when the cercopithecoid Mesopithecus replaced the hominoid Ouranopithecus along the Axios River, Greece. Because they are herbivorous and were much more abundant than primates, bovids are preferred to primates to study climate change in the Balkans as a cause of hominoid extinction. By measuring carbon stable isotope ratios of bovid enamel, we conclude that Ouranopithecus and Mesopithecus both evolved in pure C3 environments. However, the large range of δ(13)C values of apatite carbonate from bovids combined with their molar microwear and mesowear patterns preclude the presence of dense forested landscapes in northern Greece. Instead, these bovids evolved in rather open landscapes with abundant grasses in the herbaceous layer. Coldest monthly estimated temperatures were below 10°C and warmest monthly temperatures rose close to or above 20°C for the two time intervals. Oxygen isotope compositions of phosphate from bulk samples did not show significant differences between sites but did show between-species variation within each site. Different factors influence oxygen isotope composition in this context, including water provenience, feeding ecology, body mass, and rate of amelogenesis. We discuss this latter factor in regard to the high intra-tooth variations in δ(18)Op reflecting important amplitudes of seasonal variations in temperature. These estimations fit with paleobotanical data and differ slightly from estimations based on climate models. This study found no significant change in climate before and after the extinction of Ouranopithecus along the Axios River. However, strong seasonal variations with relatively cold winters were indicated, conditions quite usual for extant monkeys but unusual for great apes distributed today in inter-tropical regions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Delayed recovery of non-marine tetrapods after the end-Permian mass extinction tracks global carbon cycle

PubMed Central

Irmis, Randall B.; Whiteside, Jessica H.

2012-01-01

During the end-Permian mass extinction, marine ecosystems suffered a major drop in diversity, which was maintained throughout the Early Triassic until delayed recovery during the Middle Triassic. This depressed diversity in the Early Triassic correlates with multiple major perturbations to the global carbon cycle, interpreted as either intrinsic ecosystem or external palaeoenvironmental effects. In contrast, the terrestrial record of extinction and recovery is less clear; the effects and magnitude of the end-Permian extinction on non-marine vertebrates are particularly controversial. We use specimen-level data from southern Africa and Russia to investigate the palaeodiversity dynamics of non-marine tetrapods across the Permo-Triassic boundary by analysing sample-standardized generic richness, evenness and relative abundance. In addition, we investigate the potential effects of sampling, geological and taxonomic biases on these data. Our analyses demonstrate that non-marine tetrapods were severely affected by the end-Permian mass extinction, and that these assemblages did not begin to recover until the Middle Triassic. These data are congruent with those from land plants and marine invertebrates. Furthermore, they are consistent with the idea that unstable low-diversity post-extinction ecosystems were subject to boom–bust cycles, reflected in multiple Early Triassic perturbations of the carbon cycle. PMID:22031757

Asymmetrical nature of the Trollius-Chiastocheta interaction: insights into the evolution of nursery pollination systems.

PubMed

Suchan, Tomasz; Beauverd, Mélanie; Trim, Naïké; Alvarez, Nadir

2015-11-01

The mutualistic versus antagonistic nature of an interaction is defined by costs and benefits of each partner, which may vary depending on the environment. Contrasting with this dynamic view, several pollination interactions are considered as strictly obligate and mutualistic. Here, we focus on the interaction between Trollius europaeus and Chiastocheta flies, considered as a specialized and obligate nursery pollination system - the flies are thought to be exclusive pollinators of the plant and their larvae develop only in T. europaeus fruits. In this system, features such as the globelike flower shape are claimed to have evolved in a coevolutionary context. We examine the specificity of this pollination system and measure traits related to offspring fitness in isolated T. europaeus populations, in some of which Chiastocheta flies have gone extinct. We hypothesize that if this interaction is specific and obligate, the plant should experience dramatic drop in its relative fitness in the absence of Chiastocheta. Contrasting with this hypothesis, T. europaeus populations without flies demonstrate a similar relative fitness to those with the flies present, contradicting the putative obligatory nature of this pollination system. It also agrees with our observation that many other insects also visit and carry pollen among T. europaeus flowers. We propose that the interaction could have evolved through maximization of by-product benefits of the Chiastocheta visits, through the male flower function, and selection on floral traits by the most effective pollinator. We argue this mechanism is also central in the evolution of other nursery pollination systems.

Mutation rate evolution in replicator dynamics.

PubMed

Allen, Benjamin; Rosenbloom, Daniel I Scholes

2012-11-01

The mutation rate of an organism is itself evolvable. In stable environments, if faithful replication is costless, theory predicts that mutation rates will evolve to zero. However, positive mutation rates can evolve in novel or fluctuating environments, as analytical and empirical studies have shown. Previous work on this question has focused on environments that fluctuate independently of the evolving population. Here we consider fluctuations that arise from frequency-dependent selection in the evolving population itself. We investigate how the dynamics of competing traits can induce selective pressure on the rates of mutation between these traits. To address this question, we introduce a theoretical framework combining replicator dynamics and adaptive dynamics. We suppose that changes in mutation rates are rare, compared to changes in the traits under direct selection, so that the expected evolutionary trajectories of mutation rates can be obtained from analysis of pairwise competition between strains of different rates. Depending on the nature of frequency-dependent trait dynamics, we demonstrate three possible outcomes of this competition. First, if trait frequencies are at a mutation-selection equilibrium, lower mutation rates can displace higher ones. Second, if trait dynamics converge to a heteroclinic cycle-arising, for example, from "rock-paper-scissors" interactions-mutator strains succeed against non-mutators. Third, in cases where selection alone maintains all traits at positive frequencies, zero and nonzero mutation rates can coexist indefinitely. Our second result suggests that relatively high mutation rates may be observed for traits subject to cyclical frequency-dependent dynamics.

Dynamics of a Stochastic Predator-Prey Model with Stage Structure for Predator and Holling Type II Functional Response

NASA Astrophysics Data System (ADS)

Liu, Qun; Jiang, Daqing; Hayat, Tasawar; Alsaedi, Ahmed

2018-01-01

In this paper, we develop and study a stochastic predator-prey model with stage structure for predator and Holling type II functional response. First of all, by constructing a suitable stochastic Lyapunov function, we establish sufficient conditions for the existence and uniqueness of an ergodic stationary distribution of the positive solutions to the model. Then, we obtain sufficient conditions for extinction of the predator populations in two cases, that is, the first case is that the prey population survival and the predator populations extinction; the second case is that all the prey and predator populations extinction. The existence of a stationary distribution implies stochastic weak stability. Numerical simulations are carried out to demonstrate the analytical results.

AlGaInAs EML having high extinction ratios fabricated by identical epitaxial layer technique

NASA Astrophysics Data System (ADS)

Deng, Qiufang; Guo, Lu; Liang, Song; Sun, Siwei; Xie, Xiao; Zhu, Hongliang; Wang, Wei

2018-04-01

AlGaInAs electroabsorption-modulated lasers (EMLs) fabricated by identical epitaxial layer technique are demonstrated. The EML device shows an infinite characteristic temperature when the temperature ranges from 20 oC to 30 oC. The integrated modulator has static extinction ratios of larger than 20 dB at a reverse bias voltage of - 2 V. The small signal modulation bandwidth of the modulator is larger than 11 GHz. At 10 Gb/s data modulation, the dynamic extinction ratio is about 9.5 dB in a back to back test configuration. Because only a simple fabrication procedure is needed, our EMLs are promising low cost light sources for optical fiber transmission applications.

Dynamics of a Stochastic Predator-Prey Model with Stage Structure for Predator and Holling Type II Functional Response

NASA Astrophysics Data System (ADS)

Liu, Qun; Jiang, Daqing; Hayat, Tasawar; Alsaedi, Ahmed

2018-06-01

In this paper, we develop and study a stochastic predator-prey model with stage structure for predator and Holling type II functional response. First of all, by constructing a suitable stochastic Lyapunov function, we establish sufficient conditions for the existence and uniqueness of an ergodic stationary distribution of the positive solutions to the model. Then, we obtain sufficient conditions for extinction of the predator populations in two cases, that is, the first case is that the prey population survival and the predator populations extinction; the second case is that all the prey and predator populations extinction. The existence of a stationary distribution implies stochastic weak stability. Numerical simulations are carried out to demonstrate the analytical results.

Stochastic foundations in nonlinear density-regulation growth

NASA Astrophysics Data System (ADS)

Méndez, Vicenç; Assaf, Michael; Horsthemke, Werner; Campos, Daniel

2017-08-01

In this work we construct individual-based models that give rise to the generalized logistic model at the mean-field deterministic level and that allow us to interpret the parameters of these models in terms of individual interactions. We also study the effect of internal fluctuations on the long-time dynamics for the different models that have been widely used in the literature, such as the theta-logistic and Savageau models. In particular, we determine the conditions for population extinction and calculate the mean time to extinction. If the population does not become extinct, we obtain analytical expressions for the population abundance distribution. Our theoretical results are based on WKB theory and the probability generating function formalism and are verified by numerical simulations.

Examining the relationship between local extinction risk and position in range.

PubMed

Boakes, Elizabeth H; Isaac, Nicholas J B; Fuller, Richard A; Mace, Georgina M; McGowan, Philip J K

2018-02-01

Over half of globally threatened animal species have experienced rapid geographic range loss. Identifying the parts of species' distributions most vulnerable to local extinction would benefit conservation planning. However, previous studies give little consensus on whether ranges decline to the core or edge. We built on previous work by using empirical data to examine the position of recent local extinctions within species' geographic ranges, address range position as a continuum, and explore the influence of environmental factors. We aggregated point-locality data for 125 Galliform species from across the Palearctic and Indo-Malaya into equal-area half-degree grid cells and used a multispecies dynamic Bayesian occupancy model to estimate rates of local extinctions. Our model provides a novel approach to identify loss of populations from within species ranges. We investigated the relationship between extinction rates and distance from range edge by examining whether patterns were consistent across biogeographic realm and different categories of land use. In the Palearctic, local extinctions occurred closer to the range edge than range core in both unconverted and human-dominated landscapes. In Indo-Malaya, no pattern was found for unconverted landscapes, but in human-dominated landscapes extinctions tended to occur closer to the core than the edge. Our results suggest that local and regional factors override general spatial patterns of recent local extinction within species' ranges and highlight the difficulty of predicting the parts of a species' distribution most vulnerable to threat. © 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Environmental change preceded Caribbean extinction by 2 million years

PubMed Central

O'Dea, Aaron; Jackson, Jeremy B. C.; Fortunato, Helena; Smith, J. Travis; D'Croz, Luis; Johnson, Kenneth G.; Todd, Jonathan A.

2007-01-01

Paleontologists typically treat major episodes of extinction as single and distinct events in which a major environmental perturbation results in a synchronous evolutionary response. Alternatively, the causes of biotic change may be multifaceted and extinction may lag behind the changes ultimately responsible because of nonlinear ecological dynamics. We examined these alternatives for the major episode of Caribbean extinction 2 million years ago (Ma). Isolation of the Caribbean from the Eastern Pacific by uplift of the Panamanian Isthmus was associated with synchronous changes in Caribbean near shore environments and community composition between 4.25 and 3.45 Ma. Seasonal fluctuations in Caribbean seawater temperature decreased 3-fold, carbonate deposition increased, and there was a striking, albeit patchy, shift in dominance of benthic ecosystems from heterotrophic mollusks to mixotrophic reef corals and calcareous algae. All of these changes correspond well with a simple model of decreased upwelling and collapse in planktonic productivity associated with the final stages of the closure of the isthmian barrier. However, extinction rates of mollusks and corals did not increase until 3–2 Ma and sharply peaked between 2 and 1 Ma, even though extinction overwhelmingly affected taxa commonly associated with high productivity. This time lag suggests that something other than environmental change per se was involved in extinction that does not occur as a single event. Understanding cause and effect will require more taxonomically refined analysis of the changing abundance and distribution patterns of different ecological guilds in the 2 million years leading up to the relatively sudden peak in extinction. PMID:17369359

Dynamic analysis of a stochastic rumor propagation model

NASA Astrophysics Data System (ADS)

Jia, Fangju; Lv, Guangying

2018-01-01

The rapid development of the Internet, especially the emergence of the social networks, leads rumor propagation into a new media era. In this paper, we are concerned with a stochastic rumor propagation model. Sufficient conditions for extinction and persistence in the mean of the rumor are established. The threshold between persistence in the mean and extinction of the rumor is obtained. Compared with the corresponding deterministic model, the threshold affected by the white noise is smaller than the basic reproduction number R0 of the deterministic system.

Coexistence and survival in conservative Lotka-Volterra networks.

PubMed

Knebel, Johannes; Krüger, Torben; Weber, Markus F; Frey, Erwin

2013-04-19

Analyzing coexistence and survival scenarios of Lotka-Volterra (LV) networks in which the total biomass is conserved is of vital importance for the characterization of long-term dynamics of ecological communities. Here, we introduce a classification scheme for coexistence scenarios in these conservative LV models and quantify the extinction process by employing the Pfaffian of the network's interaction matrix. We illustrate our findings on global stability properties for general systems of four and five species and find a generalized scaling law for the extinction time.

Coexistence and Survival in Conservative Lotka-Volterra Networks

NASA Astrophysics Data System (ADS)

Knebel, Johannes; Krüger, Torben; Weber, Markus F.; Frey, Erwin

2013-04-01

Analyzing coexistence and survival scenarios of Lotka-Volterra (LV) networks in which the total biomass is conserved is of vital importance for the characterization of long-term dynamics of ecological communities. Here, we introduce a classification scheme for coexistence scenarios in these conservative LV models and quantify the extinction process by employing the Pfaffian of the network’s interaction matrix. We illustrate our findings on global stability properties for general systems of four and five species and find a generalized scaling law for the extinction time.

Periodicity of mass extinctions without an extraterrestrial cause.

PubMed

Lipowski, Adam

2005-05-01

We study a lattice model of a multispecies prey-predator system. Numerical results show that for a small mutation rate the model develops irregular long-period oscillatory behavior with sizeable changes in a number of species. The periodicity of extinctions on Earth was suggested by Raup and Sepkoski [Proc. Natl. Acad. Sci. 81, 801 (1984)], but thus far is lacking a satisfactory explanation. Our model indicates that this might be a natural consequence of the ecosystem dynamics and not the result of any extraterrestrial cause.

Tangled nature: a model of evolutionary ecology.

PubMed

Christensen, Kim; di Collobiano, Simone A; Hall, Matt; Jensen, Henrik J

2002-05-07

We discuss a simple model of co-evolution. In order to emphasize the effect of interaction between individuals, the entire population is subjected to the same physical environment. Species are emergent structures and extinction, origination and diversity are entirely a consequence of co-evolutionary interaction between individuals. For comparison, we consider both asexual and sexually reproducing populations. In either case, the system evolves through periods of hectic reorganization separated by periods of coherent stable coexistence. Copyright 2002 Elsevier Science Ltd. All rights reserved.

Increasing connectivity between metapopulation ecology and landscape ecology.

PubMed

Howell, Paige E; Muths, Erin; Hossack, Blake R; Sigafus, Brent H; Chandler, Richard B

2018-05-01

Metapopulation ecology and landscape ecology aim to understand how spatial structure influences ecological processes, yet these disciplines address the problem using fundamentally different modeling approaches. Metapopulation models describe how the spatial distribution of patches affects colonization and extinction, but often do not account for the heterogeneity in the landscape between patches. Models in landscape ecology use detailed descriptions of landscape structure, but often without considering colonization and extinction dynamics. We present a novel spatially explicit modeling framework for narrowing the divide between these disciplines to advance understanding of the effects of landscape structure on metapopulation dynamics. Unlike previous efforts, this framework allows for statistical inference on landscape resistance to colonization using empirical data. We demonstrate the approach using 11 yr of data on a threatened amphibian in a desert ecosystem. Occupancy data for Lithobates chiricahuensis (Chiricahua leopard frog) were collected on the Buenos Aires National Wildlife Refuge (BANWR), Arizona, USA from 2007 to 2017 following a reintroduction in 2003. Results indicated that colonization dynamics were influenced by both patch characteristics and landscape structure. Landscape resistance increased with increasing elevation and distance to the nearest streambed. Colonization rate was also influenced by patch quality, with semi-permanent and permanent ponds contributing substantially more to the colonization of neighboring ponds relative to intermittent ponds. Ponds that only hold water intermittently also had the highest extinction rate. Our modeling framework can be widely applied to understand metapopulation dynamics in complex landscapes, particularly in systems in which the environment between habitat patches influences the colonization process. © 2018 by the Ecological Society of America.

Chaos and crises in a model for cooperative hunting: a symbolic dynamics approach.

PubMed

Duarte, Jorge; Januário, Cristina; Martins, Nuno; Sardanyés, Josep

2009-12-01

In this work we investigate the population dynamics of cooperative hunting extending the McCann and Yodzis model for a three-species food chain system with a predator, a prey, and a resource species. The new model considers that a given fraction sigma of predators cooperates in prey's hunting, while the rest of the population 1-sigma hunts without cooperation. We use the theory of symbolic dynamics to study the topological entropy and the parameter space ordering of the kneading sequences associated with one-dimensional maps that reproduce significant aspects of the dynamics of the species under several degrees of cooperative hunting. Our model also allows us to investigate the so-called deterministic extinction via chaotic crisis and transient chaos in the framework of cooperative hunting. The symbolic sequences allow us to identify a critical boundary in the parameter spaces (K,C(0)) and (K,sigma) which separates two scenarios: (i) all-species coexistence and (ii) predator's extinction via chaotic crisis. We show that the crisis value of the carrying capacity K(c) decreases at increasing sigma, indicating that predator's populations with high degree of cooperative hunting are more sensitive to the chaotic crises. We also show that the control method of Dhamala and Lai [Phys. Rev. E 59, 1646 (1999)] can sustain the chaotic behavior after the crisis for systems with cooperative hunting. We finally analyze and quantify the inner structure of the target regions obtained with this control method for wider parameter values beyond the crisis, showing a power law dependence of the extinction transients on such critical parameters.

Population ecology of insect invasions and their management

Treesearch

Andrew M. Liebhold; Patrick C. Tobin

2008-01-01

During the establishment phase of a biological invasion, population dynamics are strongly influenced by Allee effects and stochastic dynamics, both of which may lead to extinction of low-density populations. Allee effects refer to a decline in population growth rate with a decline in abundance and can arise from various mechanisms. Strategies to eradicate newly...

Modular interdependency in complex dynamical systems.

PubMed

Watson, Richard A; Pollack, Jordan B

2005-01-01

Herbert A. Simon's characterization of modularity in dynamical systems describes subsystems as having dynamics that are approximately independent of those of other subsystems (in the short term). This fits with the general intuition that modules must, by definition, be approximately independent. In the evolution of complex systems, such modularity may enable subsystems to be modified and adapted independently of other subsystems, whereas in a nonmodular system, modifications to one part of the system may result in deleterious side effects elsewhere in the system. But this notion of modularity and its effect on evolvability is not well quantified and is rather simplistic. In particular, modularity need not imply that intermodule dependences are weak or unimportant. In dynamical systems this is acknowledged by Simon's suggestion that, in the long term, the dynamical behaviors of subsystems do interact with one another, albeit in an "aggregate" manner--but this kind of intermodule interaction is omitted in models of modularity for evolvability. In this brief discussion we seek to unify notions of modularity in dynamical systems with notions of how modularity affects evolvability. This leads to a quantifiable measure of modularity and a different understanding of its effect on evolvability.

Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics.

PubMed Central

Solé, Ricard V; Montoya, José M; Erwin, Douglas H

2002-01-01

Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems. PMID:12079530

A Unified Theory of Impact Crises and Mass Extinctions: Quantitative Tests

NASA Technical Reports Server (NTRS)

Rampino, Michael R.; Haggerty, Bruce M.; Pagano, Thomas C.

1997-01-01

Several quantitative tests of a general hypothesis linking impacts of large asteroids and comets with mass extinctions of life are possible based on astronomical data, impact dynamics, and geological information. The waiting of large-body impacts on the Earth derive from the flux of Earth-crossing asteroids and comets, and the estimated size of impacts capable of causing large-scale environmental disasters, predict that impacts of objects greater than or equal to 5 km in diameter (greater than or equal to 10 (exp 7) Mt TNT equivalent) could be sufficient to explain the record of approximately 25 extinction pulses in the last 540 Myr, with the 5 recorded major mass extinctions related to impacts of the largest objects of greater than or equal to 10 km in diameter (greater than or equal to 10(exp 8) Mt Events). Smaller impacts (approximately 10 (exp 6) Mt), with significant regional environmental effects, could be responsible for the lesser boundaries in the geologic record.

Risk of population extinction from fixation of deleterious and reverse mutations.

PubMed

Lande, R

1998-01-01

A model is developed for alternate fixations of mildly deleterious and wild-type alleles arising by forward and reverse mutation in a finite population. For almost all parameter values, this gives an equilibrium load that agrees closely with the general expression derived from diffusion theory. Nearly neutral mutations with selection coefficient a few times larger than 1/(2N(e)) do the most damage by increasing the equilibrium load. The model of alternate fixations facilitates dynamical analysis of the expected load and the mean time to extinction in a population that has been suddenly reduced from a very large size to a small size. Reverse mutation can substantially improve population viability, increasing the mean time to extinction by an order of magnitude or more, but because many mutations are irreversible the effects may not be large. Populations with initially high mean fitness and small effective size, N(e) below a few hundred individuals, may be at serious risk of extinction from fixation of deleterious mutations within 10(3) to 10(4) generations.

Species-specific responses of Late Quaternary megafauna to climate and humans

PubMed Central

Lorenzen, Eline D.; Nogués-Bravo, David; Orlando, Ludovic; Weinstock, Jaco; Binladen, Jonas; Marske, Katharine A.; Ugan, Andrew; Borregaard, Michael K.; Gilbert, M. Thomas P.; Nielsen, Rasmus; Ho, Simon Y. W.; Goebel, Ted; Graf, Kelly E.; Byers, David; Stenderup, Jesper T.; Rasmussen, Morten; Campos, Paula F.; Leonard, Jennifer A.; Koepfli, Klaus-Peter; Froese, Duane; Zazula, Grant; Stafford, Thomas W.; Aaris-Sørensen, Kim; Batra, Persaram; Haywood, Alan M.; Singarayer, Joy S.; Valdes, Paul J.; Boeskorov, Gennady; Burns, James A.; Davydov, Sergey P.; Haile, James; Jenkins, Dennis L.; Kosintsev, Pavel; Kuznetsova, Tatyana; Lai, Xulong; Martin, Larry D.; McDonald, H. Gregory; Mol, Dick; Meldgaard, Morten; Munch, Kasper; Stephan, Elisabeth; Sablin, Mikhail; Sommer, Robert S.; Sipko, Taras; Scott, Eric; Suchard, Marc A.; Tikhonov, Alexei; Willerslev, Rane; Wayne, Robert K.; Cooper, Alan; Hofreiter, Michael; Sher, Andrei; Shapiro, Beth; Rahbek, Carsten; Willerslev, Eske

2014-01-01

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary remain contentious. We use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, underscoring the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change. PMID:22048313

Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: The birth-death-diversification model.

PubMed

Drakos, Nicole E; Wahl, Lindi M

2015-12-01

Theoretical approaches are essential to our understanding of the complex dynamics of mobile genetic elements (MGEs) within genomes. Recently, the birth-death-diversification model was developed to describe the dynamics of mobile promoters (MPs), a particular class of MGEs in prokaryotes. A unique feature of this model is that genetic diversification of elements was included. To explore the implications of diversification on the longterm fate of MGE lineages, in this contribution we analyze the extinction probabilities, extinction times and equilibrium solutions of the birth-death-diversification model. We find that diversification increases both the survival and growth rate of MGE families, but the strength of this effect depends on the rate of horizontal gene transfer (HGT). We also find that the distribution of MGE families per genome is not necessarily monotonically decreasing, as observed for MPs, but may have a peak in the distribution that is related to the HGT rate. For MPs specifically, we find that new families have a high extinction probability, and predict that the number of MPs is increasing, albeit at a very slow rate. Additionally, we develop an extension of the birth-death-diversification model which allows MGEs in different regions of the genome, for example coding and non-coding, to be described by different rates. This extension may offer a potential explanation as to why the majority of MPs are located in non-promoter regions of the genome. Copyright © 2015 Elsevier Inc. All rights reserved.

Endangered plant-parrot mutualisms: seed tolerance to predation makes parrots pervasive dispersers of the Parana pine

PubMed Central

Tella, José L.; Dénes, Francisco V.; Zulian, Viviane; Prestes, Nêmora P.; Martínez, Jaime; Blanco, Guillermo; Hiraldo, Fernando

2016-01-01

Parrots are largely considered plant antagonists as they usually destroy the seeds they feed on. However, there is evidence that parrots may also act as seed dispersers. We evaluated the dual role of parrots as predators and dispersers of the Critically Endangered Parana pine (Araucaria angustifolia). Eight of nine parrot species predated seeds from 48% of 526 Parana pines surveyed. Observations of the commonest parrot indicated that 22.5% of the picked seeds were dispersed by carrying them in their beaks. Another five parrot species dispersed seeds, at an estimated average distance of c. 250 m. Dispersal distances did not differ from those observed in jays, considered the main avian dispersers. Contrary to jays, parrots often dropped partially eaten seeds. Most of these seeds were handled by parrots, and the proportion of partially eaten seeds that germinated was higher than that of undamaged seeds. This may be explained by a predator satiation effect, suggesting that the large seeds of the Parana pine evolved to attract consumers for dispersal. This represents a thus far overlooked key plant-parrot mutualism, in which both components are threatened with extinction. The interaction is becoming locally extinct long before the global extinction of the species involved. PMID:27546381

Endangered plant-parrot mutualisms: seed tolerance to predation makes parrots pervasive dispersers of the Parana pine.

PubMed

Tella, José L; Dénes, Francisco V; Zulian, Viviane; Prestes, Nêmora P; Martínez, Jaime; Blanco, Guillermo; Hiraldo, Fernando

2016-08-22

Parrots are largely considered plant antagonists as they usually destroy the seeds they feed on. However, there is evidence that parrots may also act as seed dispersers. We evaluated the dual role of parrots as predators and dispersers of the Critically Endangered Parana pine (Araucaria angustifolia). Eight of nine parrot species predated seeds from 48% of 526 Parana pines surveyed. Observations of the commonest parrot indicated that 22.5% of the picked seeds were dispersed by carrying them in their beaks. Another five parrot species dispersed seeds, at an estimated average distance of c. 250 m. Dispersal distances did not differ from those observed in jays, considered the main avian dispersers. Contrary to jays, parrots often dropped partially eaten seeds. Most of these seeds were handled by parrots, and the proportion of partially eaten seeds that germinated was higher than that of undamaged seeds. This may be explained by a predator satiation effect, suggesting that the large seeds of the Parana pine evolved to attract consumers for dispersal. This represents a thus far overlooked key plant-parrot mutualism, in which both components are threatened with extinction. The interaction is becoming locally extinct long before the global extinction of the species involved.

Mineralized periodontia in extinct relatives of mammals shed light on the evolutionary history of mineral homeostasis in periodontal tissue maintenance.

PubMed

LeBlanc, Aaron R H; Reisz, Robert R; Brink, Kirstin S; Abdala, Fernando

2016-04-01

Dental ankylosis is a rare pathological condition in mammals, however, it is prevalent in their extinct relatives, the stem mammals. This study seeks to compare the mineralized state of the periodontal attachment apparatus between stem and crown mammals and discuss its implications for the evolution of non-mineralized periodontal attachment in crown mammals, including humans. Thin sections of a fossil mammal and three stem mammals were compared to reconstruct periodontal tissue development across distantly related lineages. Comparisons revealed that the extinct relatives of mammals possessed the same periodontal tissues as those in mammals, albeit in different arrangements. The ankylotic condition in stem mammals was achieved through extensive alveolar bone deposition, which eventually contacted the root cementum, thus forming a calcified periodontal ligament. Dental ankylosis was part of the normal development of the stem mammal periodontium for millions of years prior to the evolution of a permanent gomphosis in mammals. Mammals may have evolved a permanent gomphosis by delaying the processes that produced dental ankylosis in stem mammals. Pathological ankylosis may represent a reversion to the ancestral condition, which now only forms via advanced ageing and pathology. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Constraints on food chain length arising from regional metacommunity dynamics

PubMed Central

Calcagno, Vincent; Massol, François; Mouquet, Nicolas; Jarne, Philippe; David, Patrice

2011-01-01

Classical ecological theory has proposed several determinants of food chain length, but the role of metacommunity dynamics has not yet been fully considered. By modelling patchy predator–prey metacommunities with extinction–colonization dynamics, we identify two distinct constraints on food chain length. First, finite colonization rates limit predator occupancy to a subset of prey-occupied sites. Second, intrinsic extinction rates accumulate along trophic chains. We show how both processes concur to decrease maximal and average food chain length in metacommunities. This decrease is mitigated if predators track their prey during colonization (habitat selection) and can be reinforced by top-down control of prey vital rates (especially extinction). Moreover, top-down control of colonization and habitat selection can interact to produce a counterintuitive positive relationship between perturbation rate and food chain length. Our results show how novel limits to food chain length emerge in spatially structured communities. We discuss the connections between these constraints and the ones commonly discussed, and suggest ways to test for metacommunity effects in food webs. PMID:21367786

Dynamics of an ant-plant-pollinator model

NASA Astrophysics Data System (ADS)

Wang, Yuanshi; DeAngelis, Donald L.; Nathaniel Holland, J.

2015-03-01

In this paper, we consider plant-pollinator-ant systems in which plant-pollinator interaction and plant-ant interaction are both mutualistic, but there also exists interference of pollinators by ants. The plant-pollinator interaction can be described by a Beddington-DeAngelis formula, so we extend the formula to characterize plant-pollinator mutualisms, including the interference by ants, and form a plant-pollinator-ant model. Using dynamical systems theory, we show uniform persistence of the model. Moreover, we demonstrate conditions under which boundary equilibria are globally asymptotically stable. The dynamics exhibit mechanisms by which the three species could coexist when ants interfere with pollinators. We define a threshold in ant interference. When ant interference is strong, it can drive plant-pollinator mutualisms to extinction. Furthermore, if the ants depend on pollination mutualism for their persistence, then sufficiently strong ant interference could lead to their own extinction as well. Yet, when ant interference is weak, plant-ant and plant-pollinator mutualisms can promote the persistence of one another.

Message survival and decision dynamics in a class of reactive complex systems subject to external fields

NASA Astrophysics Data System (ADS)

Rodriguez Lucatero, C.; Schaum, A.; Alarcon Ramos, L.; Bernal-Jaquez, R.

2014-07-01

In this study, the dynamics of decisions in complex networks subject to external fields are studied within a Markov process framework using nonlinear dynamical systems theory. A mathematical discrete-time model is derived using a set of basic assumptions regarding the convincement mechanisms associated with two competing opinions. The model is analyzed with respect to the multiplicity of critical points and the stability of extinction states. Sufficient conditions for extinction are derived in terms of the convincement probabilities and the maximum eigenvalues of the associated connectivity matrices. The influences of exogenous (e.g., mass media-based) effects on decision behavior are analyzed qualitatively. The current analysis predicts: (i) the presence of fixed-point multiplicity (with a maximum number of four different fixed points), multi-stability, and sensitivity with respect to the process parameters; and (ii) the bounded but significant impact of exogenous perturbations on the decision behavior. These predictions were verified using a set of numerical simulations based on a scale-free network topology.

Modeling local extinction in turbulent combustion using an embedding method

NASA Astrophysics Data System (ADS)

Knaus, Robert; Pantano, Carlos

2012-11-01

Local regions of extinction in diffusion flames, called ``flame holes,'' can reduce the efficiency of combustion and increase the production of certain pollutants. At sufficiently high speeds, a flame may also be lifted from the rim of the burner to a downstream location that may be stable. These two phenomena share a common underlying mechanism of propagation related to edge-flame dynamics where chemistry and fluid mechanics are equally important. We present a formulation that describes the formation, propagation, and growth of flames holes on the stoichiometric surface using edge flame dynamics. The boundary separating the flame from the quenched region is modeled using a progress variable defined on the moving stoichiometric surface that is embedded in the three-dimensional space using an extension algorithm. This Cartesian problem is solved using a high-order finite-volume WENO method extended to this nonconservative problem. This algorithm can track the dynamics of flame holes in a turbulent reacting-shear layer and model flame liftoff without requiring full chemistry calculations.

Predicting extinction risks under climate change: coupling stochastic population models with dynamic bioclimatic habitat models.

PubMed

Keith, David A; Akçakaya, H Resit; Thuiller, Wilfried; Midgley, Guy F; Pearson, Richard G; Phillips, Steven J; Regan, Helen M; Araújo, Miguel B; Rebelo, Tony G

2008-10-23

Species responses to climate change may be influenced by changes in available habitat, as well as population processes, species interactions and interactions between demographic and landscape dynamics. Current methods for assessing these responses fail to provide an integrated view of these influences because they deal with habitat change or population dynamics, but rarely both. In this study, we linked a time series of habitat suitability models with spatially explicit stochastic population models to explore factors that influence the viability of plant species populations under stable and changing climate scenarios in South African fynbos, a global biodiversity hot spot. Results indicate that complex interactions between life history, disturbance regime and distribution pattern mediate species extinction risks under climate change. Our novel mechanistic approach allows more complete and direct appraisal of future biotic responses than do static bioclimatic habitat modelling approaches, and will ultimately support development of more effective conservation strategies to mitigate biodiversity losses due to climate change.

Genomic evidence for large, long-lived ancestors to placental mammals.

PubMed

Romiguier, J; Ranwez, V; Douzery, E J P; Galtier, N

2013-01-01

It is widely assumed that our mammalian ancestors, which lived in the Cretaceous era, were tiny animals that survived massive asteroid impacts in shelters and evolved into modern forms after dinosaurs went extinct, 65 Ma. The small size of most Mesozoic mammalian fossils essentially supports this view. Paleontology, however, is not conclusive regarding the ancestry of extant mammals, because Cretaceous and Paleocene fossils are not easily linked to modern lineages. Here, we use full-genome data to estimate the longevity and body mass of early placental mammals. Analyzing 36 fully sequenced mammalian genomes, we reconstruct two aspects of the ancestral genome dynamics, namely GC-content evolution and nonsynonymous over synonymous rate ratio. Linking these molecular evolutionary processes to life-history traits in modern species, we estimate that early placental mammals had a life span above 25 years and a body mass above 1 kg. This is similar to current primates, cetartiodactyls, or carnivores, but markedly different from mice or shrews, challenging the dominant view about mammalian origin and evolution. Our results imply that long-lived mammals existed in the Cretaceous era and were the most successful in evolution, opening new perspectives about the conditions for survival to the Cretaceous-Tertiary crisis.

Transmissible cancer in Tasmanian devils: localized lineage replacement and host population response

PubMed Central

Hamede, Rodrigo K.; Pearse, Anne-Maree; Swift, Kate; Barmuta, Leon A.; Murchison, Elizabeth P.; Jones, Menna E.

2015-01-01

Tasmanian devil facial tumour disease (DFTD) is a clonally transmissible cancer threatening the Tasmanian devil (Sarcophilus harrisii) with extinction. Live cancer cells are the infectious agent, transmitted to new hosts when individuals bite each other. Over the 18 years since DFTD was first observed, distinct genetic and karyotypic sublineages have evolved. In this longitudinal study, we investigate the associations between tumour karyotype, epidemic patterns and host demographic response to the disease. Reduced host population effects and low DFTD infection rates were associated with high prevalence of tetraploid tumours. Subsequent replacement by a diploid variant of DFTD coincided with a rapid increase in disease prevalence, population decline and reduced mean age of the population. Our results suggest a role for tumour genetics in DFTD transmission dynamics and epidemic outcome. Future research, for this and other highly pathogenic emerging infectious diseases, should focus on understanding the evolution of host and pathogen genotypes, their effects on susceptibility and tolerance to infection, and their implications for designing novel genetic management strategies. This study provides evidence for a rapid localized lineage replacement occurring within a transmissible cancer epidemic and highlights the possibility that distinct DFTD genetic lineages may harbour traits that influence pathogen fitness. PMID:26336167

Geological implications of impacts of large asteroids and comets on the earth

NASA Technical Reports Server (NTRS)

Silver, L. T. (Editor); Schultz, P. H. (Editor)

1982-01-01

The present conference discusses such topics as large object fluxes in near-earth space and the probabilities of terrestrial impacts, the geological record of impacts, dynamics modeling for large body impacts on continents and oceans, physical, chemical, and biological models of large impacts' atmospheric effects, dispersed impact ejecta and their signatures, general considerations concerning mass biological extinctions, the Cretaceous/Tertiary boundary event, geochemical signatures in the stratigraphic record, and other phanerozoic events. Attention is given to terrestrial impact rates for long- and short-period comets, estimates of crater size for large body impact, a first-order estimate of shock heating and vaporization in oceanic impacts, atmospheric effects in the first few minutes after an impact, a feasibility test for biogeographic extinction, and the planktonic and dinosaur extinctions.

Effect of lethality on the extinction and on the error threshold of quasispecies.

PubMed

Tejero, Hector; Marín, Arturo; Montero, Francisco

2010-02-21

In this paper the effect of lethality on error threshold and extinction has been studied in a population of error-prone self-replicating molecules. For given lethality and a simple fitness landscape, three dynamic regimes can be obtained: quasispecies, error catastrophe, and extinction. Using a simple model in which molecules are classified as master, lethal and non-lethal mutants, it is possible to obtain the mutation rates of the transitions between the three regimes analytically. The numerical resolution of the extended model, in which molecules are classified depending on their Hamming distance to the master sequence, confirms the results obtained in the simple model and shows how an error catastrophe regime changes when lethality is taken in account. (c) 2009 Elsevier Ltd. All rights reserved.

Recovery of Carbonate Ecosystems Following the End-Triassic Mass Extinction: Insights from Mercury Anomalies and Their Relationship to the Central Atlantic Magmatic Province

NASA Astrophysics Data System (ADS)

Corsetti, F. A.; Thibodeau, A. M.; Ritterbush, K. A.; West, A. J.; Yager, J. A.; Ibarra, Y.; Bottjer, D. J.; Berelson, W.; Bergquist, B. A.

2015-12-01

Recent high-resolution age dating demonstrates that the end-Triassic mass extinction overlapped with the eruption of the Central Atlantic Magmatic Province (CAMP), and the release of CO2 and other volatiles to the atmosphere has been implicated in the extinction. Given the potentially massive release of CO2, ocean acidification is commonly considered a factor in the extinction and the collapse of shallow marine carbonate ecosystems. However, the timing of global marine biotic recovery versus the CAMP eruptions is more uncertain. Here, we use Hg concentrations and Hg/TOC ratios as indicators of CAMP volcanism in continental shelf sediments, the primary archive of faunal data. In Triassic-Jurassic strata, Muller Canyon, Nevada, Hg and Hg/TOC levels are low prior to the extinction, rise sharply in the extinction interval, peak just prior to the appearance of the first Jurassic ammonite, and remain above background in association with a depauperate (low diversity) earliest Jurassic fauna. The return of Hg to pre-extinction levels is associated with a significant pelagic and benthic faunal recovery. We conclude that significant biotic recovery did not begin until CAMP eruptions ceased. Furthermore, the initial benthic recovery in the Muller Canyon section involves the expansion of a siliceous sponge-dominated ecosystem across shallow marine environments, a feature now known from other sections around the world (e.g., Peru, Morocco, Austria, etc.). Carbonate dominated benthic ecosystems (heralded by the return of abundant corals and other skeletal carbonates) did not recover for ~1 million years following the last eruption of CAMP, longer than the typical duration considered for ocean acidification events, implying other factors may have played a role in carbonate ecosystem dynamics after the extinction.

To predict the niche, model colonization and extinction

USGS Publications Warehouse

Yackulic, Charles B.; Nichols, James D.; Reid, Janice; Der, Ricky

2015-01-01

Ecologists frequently try to predict the future geographic distributions of species. Most studies assume that the current distribution of a species reflects its environmental requirements (i.e., the species' niche). However, the current distributions of many species are unlikely to be at equilibrium with the current distribution of environmental conditions, both because of ongoing invasions and because the distribution of suitable environmental conditions is always changing. This mismatch between the equilibrium assumptions inherent in many analyses and the disequilibrium conditions in the real world leads to inaccurate predictions of species' geographic distributions and suggests the need for theory and analytical tools that avoid equilibrium assumptions. Here, we develop a general theory of environmental associations during periods of transient dynamics. We show that time-invariant relationships between environmental conditions and rates of local colonization and extinction can produce substantial temporal variation in occupancy–environment relationships. We then estimate occupancy–environment relationships during three avian invasions. Changes in occupancy–environment relationships over time differ among species but are predicted by dynamic occupancy models. Since estimates of the occupancy–environment relationships themselves are frequently poor predictors of future occupancy patterns, research should increasingly focus on characterizing how rates of local colonization and extinction vary with environmental conditions.

From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis.

PubMed

Lamsdell, James C; Selden, Paul A

2017-01-01

Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to a stagnant persistent lineage, pinpointing the Devonian as the period during which this evolutionary regime shift occurred. The late Devonian biotic crisis is potentially unique among the "Big Five" mass extinctions in exhibiting a drop in speciation rates rather than an increase in extinction. Our study reveals eurypterids show depressed speciation rates throughout the Devonian but no abnormal peaks in extinction. Loss of morphospace occupation is random across all Paleozoic extinction events; however, differential origination during the Devonian results in a migration and subsequent stagnation of occupied morphospace. This shift appears linked to an ecological transition from euryhaline taxa to freshwater species with low morphological diversity alongside a decrease in endemism. These results demonstrate the importance of the Devonian biotic crisis in reshaping Paleozoic ecosystems. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Sauropod dinosaurs evolved moderately sized genomes unrelated to body size.

PubMed

Organ, Chris L; Brusatte, Stephen L; Stein, Koen

2009-12-22

Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77-2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97-2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05-5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group.

What limits the morphological disparity of clades?

PubMed Central

Oyston, Jack W.; Hughes, Martin; Wagner, Peter J.; Gerber, Sylvain; Wills, Matthew A.

2015-01-01

The morphological disparity of species within major clades shows a variety of trajectory patterns through evolutionary time. However, there is a significant tendency for groups to reach their maximum disparity relatively early in their histories, even while their species richness or diversity is comparatively low. This pattern of early high-disparity suggests that there are internal constraints (e.g. developmental pleiotropy) or external restrictions (e.g. ecological competition) upon the variety of morphologies that can subsequently evolve. It has also been demonstrated that the rate of evolution of new character states decreases in most clades through time (character saturation), as does the rate of origination of novel bodyplans and higher taxa. Here, we tested whether there was a simple relationship between the level or rate of character state exhaustion and the shape of a clade's disparity profile: specifically, its centre of gravity (CG). In a sample of 93 extinct major clades, most showed some degree of exhaustion, but all continued to evolve new states up until their extinction. Projection of states/steps curves suggested that clades realized an average of 60% of their inferred maximum numbers of states. Despite a weak but significant correlation between overall levels of homoplasy and the CG of clade disparity profiles, there were no significant relationships between any of our indices of exhaustion curve shape and the clade disparity CG. Clades showing early high-disparity were no more likely to have early character saturation than those with maximum disparity late in their evolution. PMID:26640649

Sexual selection protects against extinction.

PubMed

Lumley, Alyson J; Michalczyk, Łukasz; Kitson, James J N; Spurgin, Lewis G; Morrison, Catriona A; Godwin, Joanne L; Dickinson, Matthew E; Martin, Oliver Y; Emerson, Brent C; Chapman, Tracey; Gage, Matthew J G

2015-06-25

Reproduction through sex carries substantial costs, mainly because only half of sexual adults produce offspring. It has been theorized that these costs could be countered if sex allows sexual selection to clear the universal fitness constraint of mutation load. Under sexual selection, competition between (usually) males and mate choice by (usually) females create important intraspecific filters for reproductive success, so that only a subset of males gains paternity. If reproductive success under sexual selection is dependent on individual condition, which is contingent to mutation load, then sexually selected filtering through 'genic capture' could offset the costs of sex because it provides genetic benefits to populations. Here we test this theory experimentally by comparing whether populations with histories of strong versus weak sexual selection purge mutation load and resist extinction differently. After evolving replicate populations of the flour beetle Tribolium castaneum for 6 to 7 years under conditions that differed solely in the strengths of sexual selection, we revealed mutation load using inbreeding. Lineages from populations that had previously experienced strong sexual selection were resilient to extinction and maintained fitness under inbreeding, with some families continuing to survive after 20 generations of sib × sib mating. By contrast, lineages derived from populations that experienced weak or non-existent sexual selection showed rapid fitness declines under inbreeding, and all were extinct after generation 10. Multiple mutations across the genome with individually small effects can be difficult to clear, yet sum to a significant fitness load; our findings reveal that sexual selection reduces this load, improving population viability in the face of genetic stress.

Evolving Systems and Adaptive Key Component Control

NASA Technical Reports Server (NTRS)

Frost, Susan A.; Balas, Mark J.

2009-01-01

We propose a new framework called Evolving Systems to describe the self-assembly, or autonomous assembly, of actively controlled dynamical subsystems into an Evolved System with a higher purpose. An introduction to Evolving Systems and exploration of the essential topics of the control and stability properties of Evolving Systems is provided. This chapter defines a framework for Evolving Systems, develops theory and control solutions for fundamental characteristics of Evolving Systems, and provides illustrative examples of Evolving Systems and their control with adaptive key component controllers.

Optimal interdependence enhances the dynamical robustness of complex systems.

PubMed

Singh, Rishu Kumar; Sinha, Sitabhra

2017-08-01

Although interdependent systems have usually been associated with increased fragility, we show that strengthening the interdependence between dynamical processes on different networks can make them more likely to survive over long times. By coupling the dynamics of networks that in isolation exhibit catastrophic collapse with extinction of nodal activity, we demonstrate system-wide persistence of activity for an optimal range of interdependence between the networks. This is related to the appearance of attractors of the global dynamics comprising disjoint sets ("islands") of stable activity.

Optimal interdependence enhances the dynamical robustness of complex systems

NASA Astrophysics Data System (ADS)

Singh, Rishu Kumar; Sinha, Sitabhra

2017-08-01

Although interdependent systems have usually been associated with increased fragility, we show that strengthening the interdependence between dynamical processes on different networks can make them more likely to survive over long times. By coupling the dynamics of networks that in isolation exhibit catastrophic collapse with extinction of nodal activity, we demonstrate system-wide persistence of activity for an optimal range of interdependence between the networks. This is related to the appearance of attractors of the global dynamics comprising disjoint sets ("islands") of stable activity.

Dynamics in species composition of stream fish assemblages: environmental variability and nested subsets

Treesearch

Christopher M. Taylor; Melvin L. Warren

2001-01-01

Stream landscapes are highly variable in space and time and, like terrestrial landscapes, the resources they contain are patchily distributed. Organisms may disperse among patches to fulfill life-history requirements, but biotic and abiotic factors may limit patch or locality occupancy. Thus, the dynamics of immigration and extinction determine, in part, the local...

The Allee effect, stochastic dynamics and the eradication of alien species

Treesearch

Andrew Liebhold; Jordi Bascompte; Jordi Bascompte

2003-01-01

Previous treatments of the population biology of eradication have assumed that eradication can only be achieved via 100% removal of the alien population. However, this assumption appears to be incorrect because stochastic dynamics and the Allee effect typically contribute to the extinction of very low-density populations. We explore a model that incorporates Allee...

Representation in dynamical agents.

PubMed

Ward, Ronnie; Ward, Robert

2009-04-01

This paper extends experiments by Beer [Beer, R. D. (1996). Toward the evolution of dynamical neural networks for minimally cognitive behavior. In P. Maes, M. Mataric, J. Meyer, J. Pollack, & S. Wilson (Eds.), From animals to animats 4: Proceedings of the fourth international conference on simulation of adaptive behavior (pp. 421-429). MIT Press; Beer, R. D. (2003). The dynamics of active categorical perception in an evolved model agent (with commentary and response). Adaptive Behavior, 11 (4), 209-243] with an evolved, dynamical agent to further explore the question of representation in cognitive systems. Beer's environmentally-situated visual agent was controlled by a continuous-time recurrent neural network, and evolved to perform a categorical perception task, discriminating circles from diamonds. Despite the agent's high levels of discrimination performance, Beer found no evidence of internal representation in the best-evolved agent's nervous system. Here we examine the generality of this result. We evolved an agent for shape discrimination, and performed extensive behavioral analyses to test for representation. In this case we find that agents developed to discriminate equal-width shapes exhibit what Clark [Clark, A. (1997). The dynamical challenge. Cognitive Science, 21 (4), 461-481] calls "weak-substantive representation". The agent had internal configurations that (1) were understandably related to the object in the environment, and (2) were functionally used in a task relevant way when the target was not visible to the agent.

Cataclysms and Catastrophes: A Case Study of Improving K-12 Science Education Through a University Partnership

NASA Astrophysics Data System (ADS)

Fennell, T.; Ellins, K. K.; Morris, M.; Christeson, G.

2003-12-01

The K-12 science teacher is always seeking ways of improving and updating their curriculum by integrating the latest research into their most effective classroom activities. However, the daily demands of delivering instruction to large numbers of students coupled with the rapid advances in some fields of science can often overwhelm this effort. The NSF-sponsored Cataclysms and Catastrophes curriculum, developed by scientists from the The University of Texas at Austin Institute for Geophysics (UTIG) and Bureau of Economic Geology (BEG), middle and high school teachers, and UT graduate students (NSF GK-12 fellows) working together through the GK-12 program, is a textbook example of how universities can facilitate this quest, benefiting education at both K-12 and university levels. In 1992, "The Great K-T Extinction Debate" was developed as an activity in the Planet Earth class at the Liberal Arts and Science Academy of Austin as an interdisciplinary approach to science. Taking advantage of the media attention generated by the impact scenario for the K-T extinction, the activity consists of students participating in a simulated senate hearing on the potential causes of the K-T extinction and their implications for society today. This activity not only exposes students to the wide range of science involved in understanding mass extinctions, but also to the social, political and economic implications when this science is brought into the public arena and the corresponding use of data in decision making and disaster preparedness. While "The Great K-T Extinction Debate" was always a popular and effective activity with students, it was in desperate need of updating to keep pace with the evolving scientific debate over the cause of the K-T extinction and the growing body of impact evidence discovered over the past decade. By adding two inquiry-based learning activities that use real geophysical data collected by scientists studying the buried Chicxulub feature as a culmination to the classroom debate, we developed a curriculum module on Asteroids Impacts for the Cataclysms and Catastrophes project. This approach proved to be the ideal way to update the existing Planet Earth curriculum and to provide students with opportunities to use cutting-edge, hands-on geophysical and computer techniques to understand the most up-to-date science concerning the K-T extinction event.

Extinction and persistence of a stochastic nonlinear SIS epidemic model with jumps

NASA Astrophysics Data System (ADS)

Ge, Qing; Ji, Guilin; Xu, Jiabo; Fan, Xiaolin

2016-11-01

In this paper, Brownian motion and L e ´ vy jumps are introduced to a SIS type epidemic model with nonlinear incidence rate. The dynamical behavior of the considered model is investigated. In order to reveal the extinction and permanence of the disease, two threshold values R˜0 ,R¯0 are showed. We find that if R˜0 < 1, the disease may die out, and when R¯0 > 1, the disease may be persistent. Finally, the numerical simulations are presented to illustrate our mathematical results.

The role of prestimulus activity in visual extinction.

PubMed

Urner, Maren; Sarri, Margarita; Grahn, Jessica; Manly, Tom; Rees, Geraint; Friston, Karl

2013-07-01

Patients with visual extinction following right-hemisphere damage sometimes see and sometimes miss stimuli in the left visual field, particularly when stimuli are presented simultaneously to both visual fields. Awareness of left visual field stimuli is associated with increased activity in bilateral parietal and frontal cortex. However, it is unknown why patients see or miss these stimuli. Previous neuroimaging studies in healthy adults show that prestimulus activity biases perceptual decisions, and biases in visual perception can be attributed to fluctuations in prestimulus activity in task relevant brain regions. Here, we used functional MRI to investigate whether prestimulus activity affected perception in the context of visual extinction following stroke. We measured prestimulus activity in stimulus-responsive cortical areas during an extinction paradigm in a patient with unilateral right parietal damage and visual extinction. This allowed us to compare prestimulus activity on physically identical bilateral trials that either did or did not lead to visual extinction. We found significantly increased activity prior to stimulus presentation in two areas that were also activated by visual stimulation: the left calcarine sulcus and right occipital inferior cortex. Using dynamic causal modelling (DCM) we found that both these differences in prestimulus activity and stimulus evoked responses could be explained by enhanced effective connectivity within and between visual areas, prior to stimulus presentation. Thus, we provide evidence for the idea that differences in ongoing neural activity in visually responsive areas prior to stimulus onset affect awareness in visual extinction, and that these differences are mediated by fluctuations in extrinsic and intrinsic connectivity. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Dynamically orthogonal field equations for stochastic flows and particle dynamics

DTIC Science & Technology

2011-02-01

where uncertainty ‘lives’ as well as a system of Stochastic Di erential Equations that de nes how the uncertainty evolves in the time varying stochastic ... stochastic dynamical component that are both time and space dependent, we derive a system of field equations consisting of a Partial Differential Equation...a system of Stochastic Differential Equations that defines how the stochasticity evolves in the time varying stochastic subspace. These new

AMPHIBIAN POPULATION DYNAMICS

EPA Science Inventory

Agriculture has contributed to loss of vertebrate biodiversity in many regions, including the U.S. Corn Belt. Amphibian populations, in particular, have experienced widespread and often inexplicable declines, range reductions, and extinctions. However, few attempts have been made...

Host-pathogen metapopulation dynamics suggest high elevation refugia for boreal toads

USGS Publications Warehouse

Mosher, Brittany A.; Bailey, Larissa L.; Muths, Erin L.; Huyvaert, Kathryn P

2018-01-01

Emerging infectious diseases are an increasingly common threat to wildlife. Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is an emerging infectious disease that has been linked to amphibian declines around the world. Few studies exist that explore amphibian-Bd dynamics at the landscape scale, limiting our ability to identify which factors are associated with variation in population susceptibility and to develop effective in situdisease management. Declines of boreal toads (Anaxyrus boreas boreas) in the Southern Rocky Mountains are largely attributed to chytridiomycosis but variation exists in local extinction of boreal toads across this metapopulation. Using a large-scale historic dataset, we explored several potential factors influencing disease dynamics in the boreal toad-Bd system: geographic isolation of populations, amphibian community richness, elevational differences, and habitat permanence. We found evidence that boreal toad extinction risk was lowest at high elevations where temperatures may be sub-optimal for Bd growth and where small boreal toad populations may be below the threshold needed for efficient pathogen transmission. In addition, boreal toads were more likely to recolonize high elevation sites after local extinction, again suggesting that high elevations may provide refuge from disease for boreal toads. We illustrate a modeling framework that will be useful to natural resource managers striving to make decisions in amphibian-Bdsystems. Our data suggest that in the southern Rocky Mountains high elevation sites should be prioritized for conservation initiatives like reintroductions.

The escalatory Red Queen: Population extinction and replacement following arms race dynamics in poplar rust.

PubMed

Persoons, Antoine; Hayden, Katherine J; Fabre, Bénédicte; Frey, Pascal; De Mita, Stéphane; Tellier, Aurélien; Halkett, Fabien

2017-04-01

Host-parasite systems provide convincing examples of Red Queen co-evolutionary dynamics. Yet, a key process underscored in Van Valen's theory - that arms race dynamics can result in extinction - has never been documented. One reason for this may be that most sampling designs lack the breadth needed to illuminate the rapid pace of adaptation by pathogen populations. In this study, we used a 25-year temporal sampling to decipher the demographic history of a plant pathogen: the poplar rust fungus, Melampsora larici-populina. A major adaptive event occurred in 1994 with the breakdown of R7 resistance carried by several poplar cultivars widely planted in Western Europe since 1982. The corresponding virulence rapidly spread in M. larici-populina populations and nearly reached fixation in northern France, even on susceptible hosts. Using both temporal records of virulence profiles and temporal population genetic data, our analyses revealed that (i) R7 resistance breakdown resulted in the emergence of a unique and homogeneous genetic group, the so-called cultivated population, which predominated in northern France for about 20 years, (ii) selection for Vir7 individuals brought with it multiple other virulence types via hitchhiking, resulting in an overall increase in the population-wide number of virulence types and (iii) - above all - the emergence of the cultivated population superseded the initial population which predominated at the same place before R7 resistance breakdown. Our temporal analysis illustrates how antagonistic co-evolution can lead to population extinction and replacement, hence providing direct evidence for the escalation process which is at the core of Red Queen dynamics. © 2016 John Wiley & Sons Ltd.

Stochastic population dynamics of a montane ground-dwelling squirrel.

PubMed

Hostetler, Jeffrey A; Kneip, Eva; Van Vuren, Dirk H; Oli, Madan K

2012-01-01

Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990-2008) study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis) population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1) for 9 out of 18 years. The stochastic population growth rate λ(s) was 0.92, suggesting a declining population; however, the 95% CI on λ(s) included 1.0 (0.52-1.60). Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years) probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration.

Stochastic Population Dynamics of a Montane Ground-Dwelling Squirrel

PubMed Central

Hostetler, Jeffrey A.; Kneip, Eva; Van Vuren, Dirk H.; Oli, Madan K.

2012-01-01

Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990–2008) study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis) population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1) for 9 out of 18 years. The stochastic population growth rate λs was 0.92, suggesting a declining population; however, the 95% CI on λs included 1.0 (0.52–1.60). Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years) probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration. PMID:22479616

Defining the limits of flowers: the challenge of distinguishing between the evolutionary products of simple versus compound strobili

PubMed Central

Rudall, Paula J.; Bateman, Richard M.

2010-01-01

Recent phylogenetic reconstructions suggest that axially condensed flower-like structures evolved iteratively in seed plants from either simple or compound strobili. The simple-strobilus model of flower evolution, widely applied to the angiosperm flower, interprets the inflorescence as a compound strobilus. The conifer cone and the gnetalean ‘flower’ are commonly interpreted as having evolved from a compound strobilus by extreme condensation and (at least in the case of male conifer cones) elimination of some structures present in the presumed ancestral compound strobilus. These two hypotheses have profoundly different implications for reconstructing the evolution of developmental genetic mechanisms in seed plants. If different flower-like structures evolved independently, there should intuitively be little commonality of patterning genes. However, reproductive units of some early-divergent angiosperms, including the extant genus Trithuria (Hydatellaceae) and the extinct genus Archaefructus (Archaefructaceae), apparently combine features considered typical of flowers and inflorescences. We re-evaluate several disparate strands of comparative data to explore whether flower-like structures could have arisen by co-option of flower-expressed patterning genes into independently evolved condensed inflorescences, or vice versa. We discuss the evolution of the inflorescence in both gymnosperms and angiosperms, emphasising the roles of heterotopy in dictating gender expression and heterochrony in permitting internodal compression. PMID:20047867

Defining the limits of flowers: the challenge of distinguishing between the evolutionary products of simple versus compound strobili.

PubMed

Rudall, Paula J; Bateman, Richard M

2010-02-12

Recent phylogenetic reconstructions suggest that axially condensed flower-like structures evolved iteratively in seed plants from either simple or compound strobili. The simple-strobilus model of flower evolution, widely applied to the angiosperm flower, interprets the inflorescence as a compound strobilus. The conifer cone and the gnetalean 'flower' are commonly interpreted as having evolved from a compound strobilus by extreme condensation and (at least in the case of male conifer cones) elimination of some structures present in the presumed ancestral compound strobilus. These two hypotheses have profoundly different implications for reconstructing the evolution of developmental genetic mechanisms in seed plants. If different flower-like structures evolved independently, there should intuitively be little commonality of patterning genes. However, reproductive units of some early-divergent angiosperms, including the extant genus Trithuria (Hydatellaceae) and the extinct genus Archaefructus (Archaefructaceae), apparently combine features considered typical of flowers and inflorescences. We re-evaluate several disparate strands of comparative data to explore whether flower-like structures could have arisen by co-option of flower-expressed patterning genes into independently evolved condensed inflorescences, or vice versa. We discuss the evolution of the inflorescence in both gymnosperms and angiosperms, emphasising the roles of heterotopy in dictating gender expression and heterochrony in permitting internodal compression.

Biotic and environmental dynamics through the Late Jurassic-Early Cretaceous transition: evidence for protracted faunal and ecological turnover.

PubMed

Tennant, Jonathan P; Mannion, Philip D; Upchurch, Paul; Sutton, Mark D; Price, Gregory D

2017-05-01

The Late Jurassic to Early Cretaceous interval represents a time of environmental upheaval and cataclysmic events, combined with disruptions to terrestrial and marine ecosystems. Historically, the Jurassic/Cretaceous (J/K) boundary was classified as one of eight mass extinctions. However, more recent research has largely overturned this view, revealing a much more complex pattern of biotic and abiotic dynamics than has previously been appreciated. Here, we present a synthesis of our current knowledge of Late Jurassic-Early Cretaceous events, focusing particularly on events closest to the J/K boundary. We find evidence for a combination of short-term catastrophic events, large-scale tectonic processes and environmental perturbations, and major clade interactions that led to a seemingly dramatic faunal and ecological turnover in both the marine and terrestrial realms. This is coupled with a great reduction in global biodiversity which might in part be explained by poor sampling. Very few groups appear to have been entirely resilient to this J/K boundary 'event', which hints at a 'cascade model' of ecosystem changes driving faunal dynamics. Within terrestrial ecosystems, larger, more-specialised organisms, such as saurischian dinosaurs, appear to have suffered the most. Medium-sized tetanuran theropods declined, and were replaced by larger-bodied groups, and basal eusauropods were replaced by neosauropod faunas. The ascent of paravian theropods is emphasised by escalated competition with contemporary pterosaur groups, culminating in the explosive radiation of birds, although the timing of this is obfuscated by biases in sampling. Smaller, more ecologically diverse terrestrial non-archosaurs, such as lissamphibians and mammaliaforms, were comparatively resilient to extinctions, instead documenting the origination of many extant groups around the J/K boundary. In the marine realm, extinctions were focused on low-latitude, shallow marine shelf-dwelling faunas, corresponding to a significant eustatic sea-level fall in the latest Jurassic. More mobile and ecologically plastic marine groups, such as ichthyosaurs, survived the boundary relatively unscathed. High rates of extinction and turnover in other macropredaceous marine groups, including plesiosaurs, are accompanied by the origin of most major lineages of extant sharks. Groups which occupied both marine and terrestrial ecosystems, including crocodylomorphs, document a selective extinction in shallow marine forms, whereas turtles appear to have diversified. These patterns suggest that different extinction selectivity and ecological processes were operating between marine and terrestrial ecosystems, which were ultimately important in determining the fates of many key groups, as well as the origins of many major extant lineages. We identify a series of potential abiotic candidates for driving these patterns, including multiple bolide impacts, several episodes of flood basalt eruptions, dramatic climate change, and major disruptions to oceanic systems. The J/K transition therefore, although not a mass extinction, represents an important transitional period in the co-evolutionary history of life on Earth. © 2016 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

The evolution and extinction of science fiction.

PubMed

Hrotic, Steven

2014-11-01

Science fiction literature reflects our constantly evolving attitudes towards science and technological innovations, and the kinds of societal impacts believed possible. The newly popular subgenre 'steampunk' shows that these attitudes have significantly shifted. Examined from a cognitive anthropological perspective, science fiction reveals the cultural evolution of the genre as intelligently designed, and implies a cognitive mechanism of group membership reliant on implicit memory. However, such an analysis also suggests that genre science fiction as it was in the 20th century may no longer exist. © The Author(s) 2013.

Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection.

PubMed

Janković, Srdja; Ćirković, Milan M

2016-03-01

Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.

The Hidden Lives of Nurses' Cognitive Artifacts.

PubMed

Blaz, Jacquelyn W; Doig, Alexa K; Cloyes, Kristin G; Staggers, Nancy

2016-09-07

Standardizing nursing handoffs at shift change is recommended to improve communication, with electronic tools as the primary approach. However, nurses continue to rely on personally created paper-based cognitive artifacts - their "paper brains" - to support handoffs, indicating a deficiency in available electronic versions. The purpose of this qualitative study was to develop a deep understanding of nurses' paper-based cognitive artifacts in the context of a cancer specialty hospital. After completing 73 hours of hospital unit field observations, 13 medical oncology nurses were purposively sampled, shadowed for a single shift and interviewed using a semi-structured technique. An interpretive descriptive study design guided analysis of the data corpus of field notes, transcribed interviews, images of nurses' paper-based cognitive artifacts, and analytic memos. Findings suggest nurses' paper brains are personal, dynamic, living objects that undergo a life cycle during each shift and evolve over the course of a nurse's career. The life cycle has four phases: Creation, Application, Reproduction, and Destruction. Evolution in a nurse's individually styled, paper brain is triggered by a change in the nurse's environment that reshapes cognitive needs. If a paper brain no longer provides cognitive support in the new environment, it is modified into (adapted) or abandoned (made extinct) for a different format that will provide the necessary support. The "hidden lives" - the life cycle and evolution - of paper brains have implications for the design of successful electronic tools to support nursing practice, including handoff. Nurses' paper brains provide cognitive support beyond the context of handoff. Information retrieval during handoff is undoubtedly an important function of nurses' paper brains, but tools designed to standardize handoff communication without accounting for cognitive needs during all phases of the paper brain life cycle or the ability to evolve with changes to those cognitive needs will be underutilized.

Forest fragmentation and bird community dynamics: inference at regional scales

Treesearch

Thierry Boulinier; James D. Nichols; James E. Hines; John R. Sauer; Curtis H. Flather; Kenneth H. Pollock

2001-01-01

With increasing fragmentation of natural areas and a dramatic reduction of forest cover in several parts of the world, quantifying the impact of such changes on species richness and community dynamics has been a subject of much concern. Here, we tested whether in more fragmented landscapes there was a lower number of area-sensitive species and higher local extinction...

Continental faunal exchange and the asymmetrical radiation of carnivores.

PubMed

Pires, Mathias M; Silvestro, Daniele; Quental, Tiago B

2015-10-22

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales. © 2015 The Author(s).

Continental faunal exchange and the asymmetrical radiation of carnivores

PubMed Central

Pires, Mathias M.; Silvestro, Daniele; Quental, Tiago B.

2015-01-01

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales. PMID:26490792

An extended patch-dynamic framework for food chains in fragmented landscapes

PubMed Central

Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E.; Nijs, Ivan

2016-01-01

Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

The influence of agroforestry and other land-use types on the persistence of a Sumatran tiger (Panthera tigris sumatrae) population: an individual-based model approach.

PubMed

Imron, Muhammad Ali; Herzog, Sven; Berger, Uta

2011-08-01

The importance of preserving both protected areas and their surrounding landscapes as one of the major conservation strategies for tigers has received attention over recent decades. However, the mechanism of how land-use surrounding protected areas affects the dynamics of tiger populations is poorly understood. We developed Panthera Population Persistence (PPP)--an individual-based model--to investigate the potential mechanism of the Sumatran tiger population dynamics in a protected area and under different land-use scenarios surrounding the reserve. We tested three main landscape compositions (single, combined and real land-uses of Tesso-Nilo National Park and its surrounding area) on the probability of and time to extinction of the Sumatran tiger over 20 years in Central Sumatra. The model successfully explains the mechanisms behind the population response of tigers under different habitat landscape compositions. Feeding and mating behaviours of tigers are key factors, which determined population persistence in a heterogeneous landscape. All single land-use scenarios resulted in tiger extinction but had a different probability of extinction within 20 years. If tropical forest was combined with other land-use types, the probability of extinction was smaller. The presence of agroforesty and logging concessions adjacent to protected areas encouraged the survival of tiger populations. However, with the real land-use scenario of Tesso-Nilo National Park, tigers could not survive for more than 10 years. Promoting the practice of agroforestry systems surrounding the park is probably the most reasonable way to steer land-use surrounding the Tesso-Nilo National Park to support tiger conservation.

Low-Cost Avoidance Behaviors are Resistant to Fear Extinction in Humans

PubMed Central

Vervliet, Bram; Indekeu, Ellen

2015-01-01

Elevated levels of fear and avoidance are core symptoms across the anxiety disorders. It has long been known that fear serves to motivate avoidance. Consequently, fear extinction has been the primary focus in pre-clinical anxiety research for decades, under the implicit assumption that removing the motivator of avoidance (fear) would automatically mitigate the avoidance behaviors as well. Although this assumption has intuitive appeal, it has received little scientific scrutiny. The scarce evidence from animal studies is mixed, while the assumption remains untested in humans. The current study applied an avoidance conditioning protocol in humans to investigate the effects of fear extinction on the persistence of low-cost avoidance. Online danger-safety ratings and skin conductance responses documented the dynamics of conditioned fear across avoidance and extinction phases. Anxiety- and avoidance-related questionnaires explored individual differences in rates of avoidance. Participants first learned to click a button during a predictive danger signal, in order to cancel an upcoming aversive electrical shock (avoidance conditioning). Next, fear extinction was induced by presenting the signal in the absence of shocks while button-clicks were prevented (by removing the button in Experiment 1, or by instructing not to click the button in Experiment 2). Most importantly, post-extinction availability of the button caused a significant return of avoidant button-clicks. In addition, trait-anxiety levels correlated positively with rates of avoidance during a predictive safety signal, and with the rate of pre- to post-extinction decrease during this signal. Fear measures gradually decreased during avoidance conditioning, as participants learned that button-clicks effectively canceled the shock. Preventing button-clicks elicited a sharp increase in fear, which subsequently extinguished. Fear remained low during avoidance testing, but danger-safety ratings increased again when button-clicks were subsequently prevented. Together, these results show that low-cost avoidance behaviors can persist following fear extinction and induce increased threat appraisal. On the other hand, fear extinction did reduce augmented rates of unnecessary avoidance during safety in trait-anxious individuals, and instruction-based response prevention was more effective than removal of response cues. More research is needed to characterize the conditions under which fear extinction might mitigate avoidance. PMID:26733837

Theoretical Studies of Dust in the Galactic Environment: Some Recent Advances

NASA Technical Reports Server (NTRS)

Leung, Chun Ming

1995-01-01

Dust grains, although a minor constituent, play a very important role in the thermodynamics and evolution of many astronomical objects, e.g., young and evolved stars, nebulae, interstellar clouds, and nuclei of some galaxies. Since the birth of infrared astronomy over two decades ago, significant progress has been made not only in the observations of galactic dust, but also in the theoretical studies of phenomena involving dust grains. Models with increasing degree of sophistication and physical realism (in terms of grain properties, dust formation, emission processes, and grain alignment mechanisms) have become available. Here I review recent progress made in the following areas: (1) Extinction and emission of fractal grains. (2) Dust formation in radiation-driven outflows of evolved stars. (3) Transient heating and emission of very small dust grains. Where appropriate, relevant modeling results are presented and observational implications emphasized.

The maintenance of single-locus polymorphism. IV. Models with mutation from existing alleles.

PubMed

Spencer, H G; Marks, R W

1992-01-01

The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory.

The Ethics of Human Life Extension: The Second Argument from Evolution.

PubMed

Gyngell, Chris

2015-12-01

One argument that is sometimes made against pursuing radical forms of human life extension is that such interventions will make the species less evolvable, which would be morally undesirable. In this article, I discuss the empirical and evaluative claims of this argument. I argue that radical increases in life expectancy could, in principle, reduce the evolutionary potential of human populations through both biological and cultural mechanisms. I further argue that if life extension did reduce the evolvability of the species, this will be undesirable for three reasons: (1) it may increase the species' susceptibility to extinction risks, (2) it may adversely affect institutions and practices that promote well-being, and (3) it may impede moral progress. © The Author 2015. Published by Oxford University Press, on behalf of the Journal of Medicine and Philosophy Inc. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Diversification dynamics of rhynchostomatian ciliates: the impact of seven intrinsic traits on speciation and extinction in a microbial group.

PubMed

Vďačný, Peter; Rajter, Ľubomír; Shazib, Shahed Uddin Ahmed; Jang, Seok Won; Shin, Mann Kyoon

2017-08-30

Ciliates are a suitable microbial model to investigate trait-dependent diversification because of their comparatively complex morphology and high diversity. We examined the impact of seven intrinsic traits on speciation, extinction, and net-diversification of rhynchostomatians, a group of comparatively large, predatory ciliates with proboscis carrying a dorsal brush (sensoric structure) and toxicysts (organelles used to kill the prey). Bayesian estimates under the binary-state speciation and extinction model indicate that two types of extrusomes and two-rowed dorsal brush raise diversification through decreasing extinction. On the other hand, the higher number of contractile vacuoles and their dorsal location likely increase diversification via elevating speciation rate. Particular nuclear characteristics, however, do not significantly differ in their diversification rates and hence lineages with various macronuclear patterns and number of micronuclei have similar probabilities to generate new species. Likelihood-based quantitative state diversification analyses suggest that rhynchostomatians conform to Cope's rule in that their diversity linearly grows with increasing body length and relative length of the proboscis. Comparison with other litostomatean ciliates indicates that rhynchostomatians are not among the cladogenically most successful lineages and their survival over several hundred million years could be associated with their comparatively large and complex bodies that reduce the risk of extinction.

Evolution of opercle shape in cichlid fishes from Lake Tanganyika - adaptive trait interactions in extant and extinct species flocks.

PubMed

Wilson, Laura A B; Colombo, Marco; Sánchez-Villagra, Marcelo R; Salzburger, Walter

2015-11-20

Phenotype-environment correlations and the evolution of trait interactions in adaptive radiations have been widely studied to gain insight into the dynamics underpinning rapid species diversification. In this study we explore the phenotype-environment correlation and evolution of operculum shape in cichlid fishes using an outline-based geometric morphometric approach combined with stable isotope indicators of macrohabitat and trophic niche. We then apply our method to a sample of extinct saurichthyid fishes, a highly diverse and near globally distributed group of actinopterygians occurring throughout the Triassic, to assess the utility of extant data to inform our understanding of ecomorphological evolution in extinct species flocks. A series of comparative methods were used to analyze shape data for 54 extant species of cichlids (N = 416), and 6 extinct species of saurichthyids (N = 44). Results provide evidence for a relationship between operculum shape and feeding ecology, a concentration in shape evolution towards present along with evidence for convergence in form, and significant correlation between the major axes of shape change and measures of gut length and body elongation. The operculum is one of few features that can be compared in extant and extinct groups, enabling reconstruction of phenotype-environment interactions and modes of evolutionary diversification in deep time.

Stochastic population dynamics in spatially extended predator-prey systems

NASA Astrophysics Data System (ADS)

Dobramysl, Ulrich; Mobilia, Mauro; Pleimling, Michel; Täuber, Uwe C.

2018-02-01

Spatially extended population dynamics models that incorporate demographic noise serve as case studies for the crucial role of fluctuations and correlations in biological systems. Numerical and analytic tools from non-equilibrium statistical physics capture the stochastic kinetics of these complex interacting many-particle systems beyond rate equation approximations. Including spatial structure and stochastic noise in models for predator-prey competition invalidates the neutral Lotka-Volterra population cycles. Stochastic models yield long-lived erratic oscillations stemming from a resonant amplification mechanism. Spatially extended predator-prey systems display noise-stabilized activity fronts that generate persistent correlations. Fluctuation-induced renormalizations of the oscillation parameters can be analyzed perturbatively via a Doi-Peliti field theory mapping of the master equation; related tools allow detailed characterization of extinction pathways. The critical steady-state and non-equilibrium relaxation dynamics at the predator extinction threshold are governed by the directed percolation universality class. Spatial predation rate variability results in more localized clusters, enhancing both competing species’ population densities. Affixing variable interaction rates to individual particles and allowing for trait inheritance subject to mutations induces fast evolutionary dynamics for the rate distributions. Stochastic spatial variants of three-species competition with ‘rock-paper-scissors’ interactions metaphorically describe cyclic dominance. These models illustrate intimate connections between population dynamics and evolutionary game theory, underscore the role of fluctuations to drive populations toward extinction, and demonstrate how space can support species diversity. Two-dimensional cyclic three-species May-Leonard models are characterized by the emergence of spiraling patterns whose properties are elucidated by a mapping onto a complex Ginzburg-Landau equation. Multiple-species extensions to general ‘food networks’ can be classified on the mean-field level, providing both fundamental understanding of ensuing cooperativity and profound insight into the rich spatio-temporal features and coarsening kinetics in the corresponding spatially extended systems. Novel space-time patterns emerge as a result of the formation of competing alliances; e.g. coarsening domains that each incorporate rock-paper-scissors competition games.

Dynamical Bayesian inference of time-evolving interactions: from a pair of coupled oscillators to networks of oscillators.

PubMed

Duggento, Andrea; Stankovski, Tomislav; McClintock, Peter V E; Stefanovska, Aneta

2012-12-01

Living systems have time-evolving interactions that, until recently, could not be identified accurately from recorded time series in the presence of noise. Stankovski et al. [Phys. Rev. Lett. 109, 024101 (2012)] introduced a method based on dynamical Bayesian inference that facilitates the simultaneous detection of time-varying synchronization, directionality of influence, and coupling functions. It can distinguish unsynchronized dynamics from noise-induced phase slips. The method is based on phase dynamics, with Bayesian inference of the time-evolving parameters being achieved by shaping the prior densities to incorporate knowledge of previous samples. We now present the method in detail using numerically generated data, data from an analog electronic circuit, and cardiorespiratory data. We also generalize the method to encompass networks of interacting oscillators and thus demonstrate its applicability to small-scale networks.

Analysis of operator splitting errors for near-limit flame simulations

NASA Astrophysics Data System (ADS)

Lu, Zhen; Zhou, Hua; Li, Shan; Ren, Zhuyin; Lu, Tianfeng; Law, Chung K.

2017-04-01

High-fidelity simulations of ignition, extinction and oscillatory combustion processes are of practical interest in a broad range of combustion applications. Splitting schemes, widely employed in reactive flow simulations, could fail for stiff reaction-diffusion systems exhibiting near-limit flame phenomena. The present work first employs a model perfectly stirred reactor (PSR) problem with an Arrhenius reaction term and a linear mixing term to study the effects of splitting errors on the near-limit combustion phenomena. Analysis shows that the errors induced by decoupling of the fractional steps may result in unphysical extinction or ignition. The analysis is then extended to the prediction of ignition, extinction and oscillatory combustion in unsteady PSRs of various fuel/air mixtures with a 9-species detailed mechanism for hydrogen oxidation and an 88-species skeletal mechanism for n-heptane oxidation, together with a Jacobian-based analysis for the time scales. The tested schemes include the Strang splitting, the balanced splitting, and a newly developed semi-implicit midpoint method. Results show that the semi-implicit midpoint method can accurately reproduce the dynamics of the near-limit flame phenomena and it is second-order accurate over a wide range of time step size. For the extinction and ignition processes, both the balanced splitting and midpoint method can yield accurate predictions, whereas the Strang splitting can lead to significant shifts on the ignition/extinction processes or even unphysical results. With an enriched H radical source in the inflow stream, a delay of the ignition process and the deviation on the equilibrium temperature are observed for the Strang splitting. On the contrary, the midpoint method that solves reaction and diffusion together matches the fully implicit accurate solution. The balanced splitting predicts the temperature rise correctly but with an over-predicted peak. For the sustainable and decaying oscillatory combustion from cool flames, both the Strang splitting and the midpoint method can successfully capture the dynamic behavior, whereas the balanced splitting scheme results in significant errors.

Analysis of operator splitting errors for near-limit flame simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Zhen; Zhou, Hua; Li, Shan

High-fidelity simulations of ignition, extinction and oscillatory combustion processes are of practical interest in a broad range of combustion applications. Splitting schemes, widely employed in reactive flow simulations, could fail for stiff reaction–diffusion systems exhibiting near-limit flame phenomena. The present work first employs a model perfectly stirred reactor (PSR) problem with an Arrhenius reaction term and a linear mixing term to study the effects of splitting errors on the near-limit combustion phenomena. Analysis shows that the errors induced by decoupling of the fractional steps may result in unphysical extinction or ignition. The analysis is then extended to the prediction ofmore » ignition, extinction and oscillatory combustion in unsteady PSRs of various fuel/air mixtures with a 9-species detailed mechanism for hydrogen oxidation and an 88-species skeletal mechanism for n-heptane oxidation, together with a Jacobian-based analysis for the time scales. The tested schemes include the Strang splitting, the balanced splitting, and a newly developed semi-implicit midpoint method. Results show that the semi-implicit midpoint method can accurately reproduce the dynamics of the near-limit flame phenomena and it is second-order accurate over a wide range of time step size. For the extinction and ignition processes, both the balanced splitting and midpoint method can yield accurate predictions, whereas the Strang splitting can lead to significant shifts on the ignition/extinction processes or even unphysical results. With an enriched H radical source in the inflow stream, a delay of the ignition process and the deviation on the equilibrium temperature are observed for the Strang splitting. On the contrary, the midpoint method that solves reaction and diffusion together matches the fully implicit accurate solution. The balanced splitting predicts the temperature rise correctly but with an over-predicted peak. For the sustainable and decaying oscillatory combustion from cool flames, both the Strang splitting and the midpoint method can successfully capture the dynamic behavior, whereas the balanced splitting scheme results in significant errors.« less

Impact of forestry practices at a landscape scale on the dynamics of amphibian populations.

PubMed

Harper, Elizabeth B; Patrick, David A; Gibbs, James P

2015-12-01

Forest loss is a primary cause of worldwide amphibian decline. Timber harvesting in the United States has caused dramatic changes in quality and extent of forest ecosystems, and intensive forest management still occurs. Although numerous studies have documented substantial reductions in amphibian densities related to timber harvest, subsequent extinctions are rare. To better understand the population dynamics that have allowed so many amphibian species to persist in the face of widespread forest disturbance, we developed spatially explicit metapopulation models for four forest-dependent amphibian species (Lithobates sylvaticus, Ambystoma opacum, A. talpoideum, and A. maculatum) that incorporated demographic and habitat selection data derived from experiments conducted as part of the Land Use Effects on Amphibian Populations Project (LEAP). We projected local and landscape-scale population persistence under 108 different forestry practice scenarios, varying treatment (partial cut, clear-cut with coarse woody debris [CWD] removed, and clearcut with CWD retained), cut patch size (1, 10, or 50 ha), total area cut (10, 20, or 30%), and initial amphibian population size (5, 50, or 500 adult females per local breeding population). Under these scenarios, landscape-scale extinction was highly unlikely, occurring in < 1% of model runs and for only 2 of the 4 species, because landscape-scale populations were able to persist via dispersal even despite frequent local extinctions. Yet for all species, population sizes were reduced to -50% in all clear-cut scenarios, regardless of the size of harvested patches. These findings suggest that debate over timber harvesting on pool-breeding amphibian populations in the United States should focus not on questions of landscape-scale extinction but on the ecological consequences of dramatic reductions in amphibian biomass, including changes in trophic interactions, nutrient cycling, and energy transfer. Additionally, we conclude that amphibian declines and extinctions are far more likely to occur as a result of permanent habitat loss resulting from development than from the temporary degradation of habitat caused by current forestry practices.

The roles of ecological first principles and evolutionary contingency in unraveling ecosystem response and reconstruction during the Permian-Triassic transition.

NASA Astrophysics Data System (ADS)

Roopnarine, P. D.; Weik, A.; Dineen, A.; Angielczyk, K.

2016-12-01

The Permian-Triassic mass extinction (PTME) is the most severe mass extinction recorded in Earth's history. Effects on the biosphere were complicated and often contradictory, e.g. selective species extinctions and exceptional species survival; prolonged miniaturization of some Early Triassic clades but rapid increases of size in others; and both simplified and complex trophic structures in various E. Triassic ecosystems. Here we present the results of a new generalized model of paleocommunity global stability (number of species capable of persistent coexistence in the absence of external perturbation), suggesting that community dynamics in response to species extinction, and the addition of new species in the aftermath of the PTME, is best understood as a complex outcome of predictable community dynamics and contingent, unpredictable evolutionary pathways. We applied the model to the best known PTME transitional terrestrial ecosystem, the Karoo Basin of South Africa. The model verifies previous claims that global stability scales negatively with increasing species richness and the strength of interspecific interactions. We also show that global stability scales negatively with intrinsic population growth rates. Taxon-rich Permian communities could therefore have persisted only under a restricted range of those parameters. Communities during three phases of the PTME, however, exhibited greater global stability than would be predicted from the pre-PTME communities. Those communities could therefore have maintained relative stabilities under a broader range of parameters, implying that species could have adapted by modifying life history and ecological traits with lesser negative consequences to community stability. The earliest post-PTME community with increased species richness, however, was less stable than would be predicted from pre-PTME communities. In both the extinction and aftermath communities, nonlinear deviations from the general scaling of stability result from structural features unique to those communities, perhaps limiting our ability to forecast biospheric responses to extreme perturbations.

Long-term archives reveal shifting extinction selectivity in China's postglacial mammal fauna

PubMed Central

Crees, Jennifer J.; Li, Zhipeng; Bielby, Jon; Yuan, Jing

2017-01-01

Ecosystems have been modified by human activities for millennia, and insights about ecology and extinction risk based only on recent data are likely to be both incomplete and biased. We synthesize multiple long-term archives (over 250 archaeological and palaeontological sites dating from the early Holocene to the Ming Dynasty and over 4400 historical records) to reconstruct the spatio-temporal dynamics of Holocene–modern range change across China, a megadiverse country experiencing extensive current-day biodiversity loss, for 34 mammal species over three successive postglacial time intervals. Our combined zooarchaeological, palaeontological, historical and current-day datasets reveal that both phylogenetic and spatial patterns of extinction selectivity have varied through time in China, probably in response both to cumulative anthropogenic impacts (an ‘extinction filter’ associated with vulnerable species and accessible landscapes being affected earlier by human activities) and also to quantitative and qualitative changes in regional pressures. China has experienced few postglacial global species-level mammal extinctions, and most species retain over 50% of their maximum estimated Holocene range despite millennia of increasing regional human pressures, suggesting that the potential still exists for successful species conservation and ecosystem restoration. Data from long-term archives also demonstrate that herbivores have experienced more historical extinctions in China, and carnivores have until recently displayed greater resilience. Accurate assessment of patterns of biodiversity loss and the likely predictive power of current-day correlates of faunal vulnerability and resilience is dependent upon novel perspectives provided by long-term archives. PMID:29167363

Real-time visualization of soliton molecules with evolving behavior in an ultrafast fiber laser

NASA Astrophysics Data System (ADS)

Liu, Meng; Li, Heng; Luo, Ai-Ping; Cui, Hu; Xu, Wen-Cheng; Luo, Zhi-Chao

2018-03-01

Ultrafast fiber lasers have been demonstrated to be great platforms for the investigation of soliton dynamics. The soliton molecules, as one of the most fascinating nonlinear phenomena, have been a hot topic in the field of nonlinear optics in recent years. Herein, we experimentally observed the real-time evolving behavior of soliton molecule in an ultrafast fiber laser by using the dispersive Fourier transformation technology. Several types of evolving soliton molecules were obtained in our experiments, such as soliton molecules with monotonically or chaotically evolving phase, flipping and hopping phase. These results would be helpful to the communities interested in soliton nonlinear dynamics as well as ultrafast laser technologies.

Origin of animal multicellularity: precursors, causes, consequences—the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion

PubMed Central

Cavalier-Smith, Thomas

2017-01-01

Evolving multicellularity is easy, especially in phototrophs and osmotrophs whose multicells feed like unicells. Evolving animals was much harder and unique; probably only one pathway via benthic ‘zoophytes’ with pelagic ciliated larvae allowed trophic continuity from phagocytic protozoa to gut-endowed animals. Choanoflagellate protozoa produced sponges. Converting sponge flask cells mediating larval settling to synaptically controlled nematocysts arguably made Cnidaria. I replace Haeckel's gastraea theory by a sponge/coelenterate/bilaterian pathway: Placozoa, hydrozoan diploblasty and ctenophores were secondary; stem anthozoan developmental mutations arguably independently generated coelomate bilateria and ctenophores. I emphasize animal origin's conceptual aspects (selective, developmental) related to feeding modes, cell structure, phylogeny of related protozoa, sequence evidence, ecology and palaeontology. Epithelia and connective tissue could evolve only by compensating for dramatically lower feeding efficiency that differentiation into non-choanocytes entails. Consequentially, larger bodies enabled filtering more water for bacterial food and harbouring photosynthetic bacteria, together adding more food than cell differentiation sacrificed. A hypothetical presponge of sessile triploblastic sheets (connective tissue sandwiched between two choanocyte epithelia) evolved oogamy through selection for larger dispersive ciliated larvae to accelerate benthic trophic competence and overgrowing protozoan competitors. Extinct Vendozoa might be elaborations of this organismal grade with choanocyte-bearing epithelia, before poriferan water channels and cnidarian gut/nematocysts/synapses evolved. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’. PMID:27994119

Characterizing the Norma Overdensity

NASA Astrophysics Data System (ADS)

Sargent, Benjamin; Chakrabarti, Sukanya; Boyer, Martha; Angeloni, Rodolfo; Sarajedini, Ata; Guhathakurta, Raja

2018-05-01

We recently discovered receding, clustered Cepheid candidates towards the Norma constellation that may mark a new dwarf galaxy of the Milky Way. If this dwarf galaxy is confirmed, this would be a breakthrough in near-field cosmology, as it would represent the first dwarf galaxy that was predicted by a dynamical analysis to be subsequently discovered. Underlying the search for this dwarf galaxy is the hope that one could characterize dark-matter dominated dwarf galaxies from analysis of disturbances in Galactic disks, i.e., Galactoseismology. At b 1, it would also be the closest dwarf galaxy to the Galactic plane. Aside from its expected distinct kinematics, another signature of a dwarf galaxy is an excess of stars in the CMD. When we correct for extinction the VVV photometry of the area where we saw the Cepheid candidates and subtract out a control field (i.e. a Galactic background field), we see an excess of stars that may correspond to red-clump stars at a distance of 80 kpc. However, we used the Bonifacio et al. (2000) extinction prescription that is known to be inaccurate close to the Galactic plane. Majewski et al. (2011) have shown that the combination of NIR and MIR colors, namely H-4.5 micron or K_s - 3.6 micron, can produce a far better extinction correction than prior extinction maps. To extinction correct the VVV data, we need Spitzer data that is complete down to 17 mag in 4.5 um. Deep MIR data are crucial for us to do the extinction correction properly, and Spitzer is the only instrument that can enable this effort. By appropriately correcting the VVV and F2 photometry for extinction following Majewski et al. (2011), we should be able to separate the stellar populations of the expected dwarf galaxy candidate.

Acute food deprivation enhances fear extinction but inhibits long-term depression in the lateral amygdala via ghrelin signaling.

PubMed

Huang, Chiung-Chun; Chou, Dylan; Yeh, Che-Ming; Hsu, Kuei-Sen

2016-02-01

Fear memory-encoding thalamic input synapses to the lateral amygdala (T-LA) exhibit dynamic efficacy changes that are tightly correlated with fear memory strength. Previous studies have shown that auditory fear conditioning involves strengthening of synaptic strength, and conversely, fear extinction training leads to T-LA synaptic weakening and occlusion of long-term depression (LTD) induction. These findings suggest that the mechanisms governing LTD at T-LA synapses may determine the behavioral outcomes of extinction training. Here, we explored this hypothesis by implementing food deprivation (FD) stress in mice to determine its effects on fear extinction and LTD induction at T-LA synapses. We found that FD increased plasma acylated ghrelin levels and enhanced fear extinction and its retention. Augmentation of fear extinction by FD was blocked by pretreatment with growth hormone secretagogue receptor type-1a antagonist D-Lys(3)-GHRP-6, suggesting an involvement of ghrelin signaling. Confirming previous findings, two distinct forms of LTD coexist at thalamic inputs to LA pyramidal neurons that can be induced by low-frequency stimulation (LFS) or paired-pulse LFS (PP-LFS) paired with postsynaptic depolarization, respectively. Unexpectedly, we found that FD impaired the induction of PP-LFS- and group I metabotropic glutamate receptor agonist (S)-3,5-dihydroxyphenylglycine (DHPG)-induced LTD, but not LFS-induced LTD. Ghrelin mimicked the effects of FD to impair the induction of PP-LFS- and DHPG-induced LTD at T-LA synapses, which were blocked by co-application of D-Lys(3)-GHRP-6. The sensitivity of synaptic transmission to 1-naphthyl acetyl spermine was not altered by either FD or ghrelin treatment. These results highlight distinct features of fear extinction and LTD at T-LA synapses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Perspectives on global change theory

USDA-ARS?s Scientific Manuscript database

Human-caused global changes in ecological drivers, such as carbon dioxide concentrations, climate, and nitrogen deposition, as well as direct human impacts (land use change, species movements and extinctions, etc.) are increasingly recognized as key to understanding contemporary ecosystem dynamics, ...

Global Catastrophes in Earth History: An Interdisciplinary Conference on Impacts, Volcanism, and Mass Mortality

NASA Technical Reports Server (NTRS)

1988-01-01

Topics addressed include: Cretaceous-Tertiary mass extinctions; geologial indicators for meteorite collisions; carbon dioxide catastrophes; volcanism; climatic changes; geochemistry; mineralogy; fossil records; biospheric traumas; stratigraphy; mathematical models; and ocean dynamics.

The FMOS-COSMOS survey of star-forming galaxies at z ∼ 1.6. II. The mass-metallicity relation and the dependence on star formation rate and dust extinction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zahid, H. J.; Sanders, D. B.; Chu, J.

We investigate the relationships between stellar mass, gas-phase oxygen abundance (metallicity), star formation rate (SFR), and dust content of star-forming galaxies at z ∼ 1.6 using Subaru/FMOS spectroscopy in the COSMOS field. The mass-metallicity (MZ) relation at z ∼ 1.6 is steeper than the relation observed in the local universe. The steeper MZ relation at z ∼ 1.6 is mainly due to evolution in the stellar mass where the MZ relation begins to turnover and flatten. This turnover mass is 1.2 dex larger at z ∼ 1.6. The most massive galaxies at z ∼ 1.6 (∼10{sup 11} M {sub ☉})more » are enriched to the level observed in massive galaxies in the local universe. The MZ relation we measure at z ∼ 1.6 supports the suggestion of an empirical upper metallicity limit that does not significantly evolve with redshift. We find an anti-correlation between metallicity and SFR for galaxies at a fixed stellar mass at z ∼ 1.6, which is similar to trends observed in the local universe. We do not find a relation between stellar mass, metallicity, and SFR that is independent of redshift; rather, our data suggest that there is redshift evolution in this relation. We examine the relation between stellar mass, metallicity, and dust extinction, and find that at a fixed stellar mass, dustier galaxies tend to be more metal rich. From examination of the stellar masses, metallicities, SFRs, and dust extinctions, we conclude that stellar mass is most closely related to dust extinction.« less

The evolution of giant flightless birds and novel phylogenetic relationships for extinct fowl (Aves, Galloanseres)

NASA Astrophysics Data System (ADS)

Worthy, Trevor H.; Degrange, Federico J.; Handley, Warren D.; Lee, Michael S. Y.

2017-10-01

The extinct dromornithids, gastornithids and phorusrhacids are among the most spectacular birds to have ever lived, with some giants exceeding 500 kg. The affinities and evolution of these and other related extinct birds remain contentious, with previous phylogenetic analyses being affected by widespread convergence and limited taxon sampling. We address these problems using both parsimony and tip-dated Bayesian approaches on an expansive taxon set that includes all key extinct flightless and flighted (e.g. Vegavis and lithornithids) forms, an extensive array of extant fowl (Galloanseres), representative Neoaves and palaeognaths. The Paleogene volant Lithornithidae are recovered as stem palaeognaths in the Bayesian analyses. The Galloanseres comprise four clades inferred to have diverged in the Late Cretaceous on Gondwana. In addition to Anseriformes and Galliformes, we recognize a robust new clade (Gastornithiformes) for the giant flightless Dromornithidae (Australia) and Gastornithidae (Eurasia, North America). This clade exhibits parallels to ratite palaeognaths in that flight presumably was lost and giant size attained multiple times. A fourth clade is represented by the Cretaceous Vegavis (Antarctica), which was strongly excluded from Anseriformes; thus, a crucial molecular calibration point needs to be reconsidered. The presbyornithids Wilaru (Australia) and Presbyornis (Northern Hemisphere) are robustly found to be the sister group to Anatoidea (Anseranatidae + Anatidae), a relatively more basal position than hitherto recognized. South America's largest bird, Brontornis, is not a galloansere, but a member of Neoaves related to Cariamiformes; therefore, giant Galloanseres remain unknown from this continent. Trait analyses showed that while gigantism and flightlessness evolved repeatedly in groups, diet is constrained by phylogeny: all giant Galloanseres and palaeognaths are herbivores or mainly herbivorous, and giant neoavians are zoophagous or omnivorous.

Synchrony in Metapopulations with Sporadic Dispersal

NASA Astrophysics Data System (ADS)

Jeter, Russell; Belykh, Igor

2015-06-01

We study synchronization in ecological networks under the realistic assumption that the coupling among the patches is sporadic/stochastic and due to rare and short-term meteorological conditions. Each patch is described by a tritrophic food chain model, representing the producer, consumer, and predator. If all three species can migrate, we rigorously prove that the network can synchronize as long as the migration occurs frequently, i.e. fast compared to the period of the ecological cycle, even though the network is disconnected most of the time. In the case where only the top trophic level (i.e. the predator) can migrate, we reveal an unexpected range of intermediate switching frequencies where synchronization becomes stable in a network which switches between two nonsynchronous dynamics. As spatial synchrony increases the danger of extinction, this counterintuitive effect of synchrony emerging from slower switching dispersal can be destructive for overall metapopulation persistence, presumably expected from switching between two dynamics which are unfavorable to extinction.

Antibiotic-induced population fluctuations and stochastic clearance of bacteria

PubMed Central

Le, Dai; Şimşek, Emrah; Chaudhry, Waqas

2018-01-01

Effective antibiotic use that minimizes treatment failures remains a challenge. A better understanding of how bacterial populations respond to antibiotics is necessary. Previous studies of large bacterial populations established the deterministic framework of pharmacodynamics. Here, characterizing the dynamics of population extinction, we demonstrated the stochastic nature of eradicating bacteria with antibiotics. Antibiotics known to kill bacteria (bactericidal) induced population fluctuations. Thus, at high antibiotic concentrations, the dynamics of bacterial clearance were heterogeneous. At low concentrations, clearance still occurred with a non-zero probability. These striking outcomes of population fluctuations were well captured by our probabilistic model. Our model further suggested a strategy to facilitate eradication by increasing extinction probability. We experimentally tested this prediction for antibiotic-susceptible and clinically-isolated resistant bacteria. This new knowledge exposes fundamental limits in our ability to predict bacterial eradication. Additionally, it demonstrates the potential of using antibiotic concentrations that were previously deemed inefficacious to eradicate bacteria. PMID:29508699

Evolutionary dynamics of plants and animals: a comparative approach

NASA Technical Reports Server (NTRS)

Valentine, J. W.; Tiffney, B. H.; Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

1991-01-01

Patterns of longevity and rate of appearance of taxa in the fossil record indicate a different evolutionary dynamic between land plants and marine invertebrates. Among marine invertebrates, rates of taxonomic turnover declined through the Phanerozoic, with increasingly extinction-resistant, long-lived, clades coming to dominate. Among terrestrial vascular plants, rates of turnover increased through the Phanerozoic, with short-lived, extinction-prone clades coming to dominate from the Devonian to the present. Terrestrial vertebrates appear to approximate the marine invertebrate pattern more closely than the plant record. We identify two features which individually or jointly may have influenced this distinction. First, land plants continuously invaded stressful environments during their evolution, while marine invertebrates and terrestrial vertebrates did not. Second, the relative structural simplicity and indeterminate mode of plant growth vs. the relative structural complexity and determinate mode of animal growth may have influenced the timing of major clade origin in the two groups.

Omnivory in birds is a macroevolutionary sink

PubMed Central

Burin, Gustavo; Kissling, W. Daniel; Guimarães, Paulo R.; Şekercioğlu, Çağan H.; Quental, Tiago B.

2016-01-01

Diet is commonly assumed to affect the evolution of species, but few studies have directly tested its effect at macroevolutionary scales. Here we use Bayesian models of trait-dependent diversification and a comprehensive dietary database of all birds worldwide to assess speciation and extinction dynamics of avian dietary guilds (carnivores, frugivores, granivores, herbivores, insectivores, nectarivores, omnivores and piscivores). Our results suggest that omnivory is associated with higher extinction rates and lower speciation rates than other guilds, and that overall net diversification is negative. Trait-dependent models, dietary similarity and network analyses show that transitions into omnivory occur at higher rates than into any other guild. We suggest that omnivory acts as macroevolutionary sink, where its ephemeral nature is retrieved through transitions from other guilds rather than from omnivore speciation. We propose that these dynamics result from competition within and among dietary guilds, influenced by the deep-time availability and predictability of food resources. PMID:27052750

Population dynamics of obligate cooperators

PubMed Central

Courchamp, F.; Grenfell, B.; Clutton-Brock, T.

1999-01-01

Obligate cooperative breeding species demonstrate a high rate of group extinction, which may be due to the existence of a critical number of helpers below which the group cannot subsist. Through a simple model, we study the population dynamics of obligate cooperative breeding species, taking into account the existence of a lower threshold below which the instantaneous growth rate becomes negative. The model successively incorporates (i) a distinction between species that need helpers for reproduction, survival or both, (ii) the existence of a migration rate accounting for dispersal, and (iii) stochastic mortality to simulate the effects of random catastrophic events. Our results suggest that the need for a minimum number of helpers increases the risk of extinction for obligate cooperative breeding species. The constraint imposed by this threshold is higher when helpers are needed for reproduction only or for both reproduction and survival. By driving them below this lower threshold, stochastic mortality of lower amplitude and/or lower frequency than for non-cooperative breeders may be sufficient to cause the extinction of obligate cooperative breeding groups. Migration may have a buffering effect only for groups where immigration is higher than emigration; otherwise (when immigrants from nearby groups are not available) it lowers the difference between actual group size and critical threshold, thereby constituting a higher constraint.

Synchronization and survival of connected bacterial populations

NASA Astrophysics Data System (ADS)

Gokhale, Shreyas; Conwill, Arolyn; Ranjan, Tanvi; Gore, Jeff

Migration plays a vital role in controlling population dynamics of species occupying distinct habitat patches. While local populations are vulnerable to extinction due to demographic or environmental stochasticity, migration from neighboring habitat patches can rescue these populations through colonization of uninhabited regions. However, a large migratory flux can synchronize the population dynamics in connected patches, thereby enhancing the risk of global extinction during periods of depression in population size. Here, we investigate this trade-off between local rescue and global extinction experimentally using laboratory populations of E. coli bacteria. Our model system consists of co-cultures of ampicillin resistant and chloramphenicol resistant strains that form a cross-protection mutualism and exhibit period-3 oscillations in the relative population density in the presence of both antibiotics. We quantify the onset of synchronization of oscillations in a pair of co-cultures connected by migration and demonstrate that period-3 oscillations can be disturbed for moderate rates of migration. These features are consistent with simulations of a mechanistic model of antibiotic deactivation in our system. The simulations further predict that the probability of survival of connected populations in high concentrations of antibiotics is maximized at intermediate migration rates. We verify this prediction experimentally and show that survival is enhanced through a combination of disturbance of period-3 oscillations and stochastic re-colonization events.

Host persistence or extinction from emerging infectious disease: insights from white-nose syndrome in endemic and invading regions

PubMed Central

Hoyt, Joseph R.; Langwig, Kate E.; Sun, Keping; Lu, Guanjun; Parise, Katy L.; Jiang, Tinglei; Foster, Jeffrey T.; Feng, Jiang; Kilpatrick, A. Marm

2016-01-01

Predicting species' fates following the introduction of a novel pathogen is a significant and growing problem in conservation. Comparing disease dynamics between introduced and endemic regions can offer insight into which naive hosts will persist or go extinct, with disease acting as a filter on host communities. We examined four hypothesized mechanisms for host–pathogen persistence by comparing host infection patterns and environmental reservoirs for Pseudogymnoascus destructans (the causative agent of white-nose syndrome) in Asia, an endemic region, and North America, where the pathogen has recently invaded. Although colony sizes of bats and hibernacula temperatures were very similar, both infection prevalence and fungal loads were much lower on bats and in the environment in Asia than North America. These results indicate that transmission intensity and pathogen growth are lower in Asia, likely due to higher host resistance to pathogen growth in this endemic region, and not due to host tolerance, lower transmission due to smaller populations, or lower environmentally driven pathogen growth rate. Disease filtering also appears to be favouring initially resistant species in North America. More broadly, determining the mechanisms allowing species persistence in endemic regions can help identify species at greater risk of extinction in introduced regions, and determine the consequences for disease dynamics and host–pathogen coevolution. PMID:26962138

Experimental Beetle Metapopulations Respond Positively to Dynamic Landscapes and Reduced Connectivity

PubMed Central

Govindan, Byju N.; Swihart, Robert K.

2012-01-01

Interactive effects of multiple environmental factors on metapopulation dynamics have received scant attention. We designed a laboratory study to test hypotheses regarding interactive effects of factors affecting the metapopulation dynamics of red flour beetle, Tribolium castaneum. Within a four-patch landscape we modified resource level (constant and diminishing), patch connectivity (high and low) and patch configuration (static and dynamic) to conduct a 23 factorial experiment, consisting of 8 metapopulations, each with 3 replicates. For comparison, two control populations consisting of isolated and static subpopulations were provided with resources at constant or diminishing levels. Longitudinal data from 22 tri-weekly counts of beetle abundance were analyzed using Bayesian Poisson generalized linear mixed models to estimate additive and interactive effects of factors affecting abundance. Constant resource levels, low connectivity and dynamic patches yielded greater levels of adult beetle abundance. For a given resource level, frequency of colonization exceeded extinction in landscapes with dynamic patches when connectivity was low, thereby promoting greater patch occupancy. Negative density dependence of pupae on adults occurred and was stronger in landscapes with low connectivity and constant resources; these metapopulations also demonstrated greatest stability. Metapopulations in control landscapes went extinct quickly, denoting lower persistence than comparable landscapes with low connectivity. When landscape carrying capacity was constant, habitat destruction coupled with low connectivity created asynchronous local dynamics and refugia within which cannibalism of pupae was reduced. Increasing connectivity may be counter-productive and habitat destruction/recreation may be beneficial to species in some contexts. PMID:22509314

Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium

PubMed Central

Buckley, Michael; Fariña, Richard A.; Lawless, Craig; Tambusso, P. Sebastián; Varela, Luciano; Carlini, Alfredo A.; Powell, Jaime E.; Martinez, Jorge G.

2015-01-01

For over 200 years, fossils of bizarre extinct creatures have been described from the Americas that have ranged from giant ground sloths to the ‘native’ South American ungulates, groups of mammals that evolved in relative isolation on South America. Ground sloths belong to the South American xenarthrans, a group with modern although morphologically and ecologically very different representatives (anteaters, armadillos and sloths), which has been proposed to be one of the four main eutherian clades. Recently, proteomics analyses of bone collagen have recently been used to yield a molecular phylogeny for a range of mammals including the unusual ‘Malagasy aardvark’ shown to be most closely related to the afrotherian tenrecs, and the south American ungulates supporting their morphological association with condylarths. However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested. For comparison, this paper examines the phylogenetic potential of proteomics-based sequencing through the analysis of collagen extracted from two extinct giant ground sloths, Lestodon and Megatherium. The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium. These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival. PMID:26540101

The effect of area size and predation on the time to extinction of prairie vole populations. simulation studies via SERDYCA: a Spatially-Explicit Individual-Based Model of Rodent Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostova, T; Carlsen, T

2003-11-21

We present a spatially-explicit individual-based computational model of rodent dynamics, customized for the prairie vole species, M. Ochrogaster. The model is based on trophic relationships and represents important features such as territorial competition, mating behavior, density-dependent predation and dispersal out of the modeled spatial region. Vegetation growth and vole fecundity are dependent on climatic components. The results of simulations show that the model correctly predicts the overall temporal dynamics of the population density. Time-series analysis shows a very good match between the periods corresponding to the peak population density frequencies predicted by the model and the ones reported in themore » literature. The model is used to study the relation between persistence, landscape area and predation. We introduce the notions of average time to extinction (ATE) and persistence frequency to quantify persistence. While the ATE decreases with decrease of area, it is a bell-shaped function of the predation level: increasing for 'small' and decreasing for 'large' predation levels.« less

Evolutionary dynamics of taxonomic structure

PubMed Central

Foote, Michael

2012-01-01

The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth–death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record. PMID:21865239

Spatial synchrony of local populations has increased in association with the recent Northern Hemisphere climate trend.

PubMed

Post, Eric; Forchhammer, Mads C

2004-06-22

According to ecological theory, populations whose dynamics are entrained by environmental correlation face increased extinction risk as environmental conditions become more synchronized spatially. This prediction is highly relevant to the study of ecological consequences of climate change. Recent empirical studies have indicated, for example, that large-scale climate synchronizes trophic interactions and population dynamics over broad spatial scales in freshwater and terrestrial systems. Here, we present an analysis of century-scale, spatially replicated data on local weather and the population dynamics of caribou in Greenland. Our results indicate that spatial autocorrelation in local weather has increased with large-scale climatic warming. This increase in spatial synchrony of environmental conditions has been matched, in turn, by an increase in the spatial synchrony of local caribou populations toward the end of the 20th century. Our results indicate that spatial synchrony in environmental conditions and the populations influenced by them are highly variable through time and can increase with climatic warming. We suggest that if future warming can increase population synchrony, it may also increase extinction risk.

On extinction time of a generalized endemic chain-binomial model.

PubMed

Aydogmus, Ozgur

2016-09-01

We considered a chain-binomial epidemic model not conferring immunity after infection. Mean field dynamics of the model has been analyzed and conditions for the existence of a stable endemic equilibrium are determined. The behavior of the chain-binomial process is probabilistically linked to the mean field equation. As a result of this link, we were able to show that the mean extinction time of the epidemic increases at least exponentially as the population size grows. We also present simulation results for the process to validate our analytical findings. Copyright © 2016 Elsevier Inc. All rights reserved.

A unified theory of impact crises and mass extinctions: quantitative tests.

PubMed

Rampino, M R; Haggerty, B M; Pagano, T C

1997-05-30

Several quantitative tests of a general hypothesis linking impacts of large asteroids and comets with mass extinctions of life are possible based on astronomical data, impact dynamics, and geological information. The waiting times of large-body impacts on the Earth derived from the flux of Earth-crossing asteroids and comets, and the estimated size of impacts capable of causing, large-scale environmental disasters, predict the impacts of objects > or = 5 km in diameter (> or = 10(7) Mt TNT equivalent) could be sufficient to explain the record of approximately 25 extinction pulses in the last 540 Myr, with the 5 recorded major mass extinctions related to impacts of the largest objects of > or = 10 km in diameter (> or = 10(8) Mt events). Smaller impacts (approximately 10(6) Mt), with significant regional environmental effects, could be responsible for the lesser boundaries in the geologic record. Tests of the "kill curve" relationship for impact-induced extinctions based on new data on extinction intensities, and several well-dated large impact craters, also suggest that major mass extinctions require large impacts, and that a step in the kill curve may exist at impacts that produce craters of approximately 100 km diameter, smaller impacts being capable of only relatively weak extinction pulses. Single impact craters less than approximately 60 km in diameter should not be associated with detectable global extinction pulses (although they may explain stage and zone boundaries marked by lesser faunal turnover), but multiple impacts in that size range may produce significant stepped extinction pulses. Statistical tests of the last occurrences of species at mass-extinction boundaries are generally consistent with predictions for abrupt or stepped extinctions, and several boundaries are known to show "catastrophic" signatures of environmental disasters and biomass crash, impoverished postextinction fauna and flora dominated by stress-tolerant and opportunistic species, and gradual ecological recovery and radiation of new taxa. Isotopic and other geochemical signatures are also generally consistent with the expected after-effects of catastrophic impacts. Seven of the recognized extinction pulses seem to be associated with concurrent (in some cases multiple) stratigraphic impact markers (e.g., layers with high iridium, shocked minerals, microtektites), and/or large, dated impact craters. Other less well-studied crisis intervals show elevated iridium, but well below that of the K/T spike, which might be explained by low-Ir impactors, ejecta blowoff, or sedimentary reworking and dilution of impact signatures. The best explanation for a possible periodic component of approximately 30 Myr in mass extinctions and clusters of impacts is the pulselike modulation of the comet flux associated with the solar system's periodic passage through the plane of the Milky Way Galaxy. The quantitative agreement between paleontologic and astronomical data suggests an important underlying unification of the processes involved.

Dynamical Bayesian inference of time-evolving interactions: From a pair of coupled oscillators to networks of oscillators

NASA Astrophysics Data System (ADS)

Duggento, Andrea; Stankovski, Tomislav; McClintock, Peter V. E.; Stefanovska, Aneta

2012-12-01

Living systems have time-evolving interactions that, until recently, could not be identified accurately from recorded time series in the presence of noise. Stankovski [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.109.024101 109, 024101 (2012)] introduced a method based on dynamical Bayesian inference that facilitates the simultaneous detection of time-varying synchronization, directionality of influence, and coupling functions. It can distinguish unsynchronized dynamics from noise-induced phase slips. The method is based on phase dynamics, with Bayesian inference of the time-evolving parameters being achieved by shaping the prior densities to incorporate knowledge of previous samples. We now present the method in detail using numerically generated data, data from an analog electronic circuit, and cardiorespiratory data. We also generalize the method to encompass networks of interacting oscillators and thus demonstrate its applicability to small-scale networks.

Avian response to shade‐layer restoration in coffee plantations in Puerto Rico

USGS Publications Warehouse

Irizarry, Amarilys D.; Collazo, Jaime A.; Pacifici, Krishna; Reich, Brian J.; Battle, Kathryn E.

2018-01-01

Documenting the evolving processes associated with habitat restoration and how long it takes to detect avian demographic responses is crucial to evaluate the success of restoration initiatives and to identify ways to improve their effectiveness. The importance of this endeavor prompted the U.S. Fish and Wildlife Service and the USDA Natural Resources Conservation Service to evaluate their sun‐to‐shade coffee restoration program in Puerto Rico initiated in 2003. We quantified the responses of 12 resident avian species using estimates of local occupancy and extinction probabilities based on surveys conducted in 2015–2017 at 65 restored farms grouped according to time‐since‐initial‐restoration (TSIR): new (2011–2014), intermediate (2007–2010), and old (2003–2006). We also surveyed 40 forest sites, which served as reference sites. Vegetation complexity increased with TSIR, ranging between 35 and 40% forest cover in farms 6–9 years TSIR. Forest specialists (e.g. Loxigilla portoricencis) exhibited highest average occupancy in farms initially classified as intermediate (6–9 years) and old (>10 years), paralleling occupancy in secondary forests. Occupancy of open‐habitat specialists (e.g. Tiaris olivaceus) was more variable, but higher in recently restored farms. Restoring the shade layer has the potential to heighten ecological services derived from forest specialists (e.g. frugivores) without losing the services of many open‐habitat specialists (e.g. insectivores). Annual local extinction probability for forest specialists decreased with increasing habitat complexity, strengthening the potential value of shade restoration as a tool to enhance habitat for avifauna that evolved in forested landscapes.

Sauropod dinosaurs evolved moderately sized genomes unrelated to body size

PubMed Central

Organ, Chris L.; Brusatte, Stephen L.; Stein, Koen

2009-01-01

Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77–2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97–2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05–5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group. PMID:19793755

Dynamic Optical Grating Device and Associated Method for Modulating Light

NASA Technical Reports Server (NTRS)

Park, Yeonjoon (Inventor); Choi, Sang H. (Inventor); King, Glen C. (Inventor); Chu, Sang-Hyon (Inventor)

2012-01-01

A dynamic optical grating device and associated method for modulating light is provided that is capable of controlling the spectral properties and propagation of light without moving mechanical components by the use of a dynamic electric and/or magnetic field. By changing the electric field and/or magnetic field, the index of refraction, the extinction coefficient, the transmittivity, and the reflectivity fo the optical grating device may be controlled in order to control the spectral properties of the light reflected or transmitted by the device.

Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis.

PubMed

Faith, Daniel P

2008-12-01

New species conservation strategies, including the EDGE of Existence (EDGE) program, have expanded threatened species assessments by integrating information about species' phylogenetic distinctiveness. Distinctiveness has been measured through simple scores that assign shared credit among species for evolutionary heritage represented by the deeper phylogenetic branches. A species with a high score combined with a high extinction probability receives high priority for conservation efforts. Simple hypothetical scenarios for phylogenetic trees and extinction probabilities demonstrate how such scoring approaches can provide inefficient priorities for conservation. An existing probabilistic framework derived from the phylogenetic diversity measure (PD) properly captures the idea of shared responsibility for the persistence of evolutionary history. It avoids static scores, takes into account the status of close relatives through their extinction probabilities, and allows for the necessary updating of priorities in light of changes in species threat status. A hypothetical phylogenetic tree illustrates how changes in extinction probabilities of one or more species translate into changes in expected PD. The probabilistic PD framework provided a range of strategies that moved beyond expected PD to better consider worst-case PD losses. In another example, risk aversion gave higher priority to a conservation program that provided a smaller, but less risky, gain in expected PD. The EDGE program could continue to promote a list of top species conservation priorities through application of probabilistic PD and simple estimates of current extinction probability. The list might be a dynamic one, with all the priority scores updated as extinction probabilities change. Results of recent studies suggest that estimation of extinction probabilities derived from the red list criteria linked to changes in species range sizes may provide estimated probabilities for many different species. Probabilistic PD provides a framework for single-species assessment that is well-integrated with a broader measurement of impacts on PD owing to climate change and other factors.

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics

PubMed Central

Campos, Paula F.; Willerslev, Eske; Sher, Andrei; Orlando, Ludovic; Axelsson, Erik; Tikhonov, Alexei; Aaris-Sørensen, Kim; Greenwood, Alex D.; Kahlke, Ralf-Dietrich; Kosintsev, Pavel; Krakhmalnaya, Tatiana; Kuznetsova, Tatyana; Lemey, Philippe; MacPhee, Ross; Norris, Christopher A.; Shepherd, Kieran; Suchard, Marc A.; Zazula, Grant D.; Shapiro, Beth; Gilbert, M. Thomas P.

2010-01-01

The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at ≈45,000 radiocarbon years before present (14C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 14C YBP, recontracted at ca. 18,000 14C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations. PMID:20212118

Comparison of reintroduction and enhancement effects on metapopulation viability

USGS Publications Warehouse

Halsey, Samniqueka J; Bell, Timothy J.; McEachern, A. Kathryn; Pavlovic, Noel B.

2015-01-01

Metapopulation viability depends upon a balance of extinction and colonization of local habitats by a species. Mechanisms that can affect this balance include physical characteristics related to natural processes (e.g. succession) as well as anthropogenic actions. Plant restorations can help to produce favorable metapopulation dynamics and consequently increase viability; however, to date no studies confirm this is true. Population viability analysis (PVA) allows for the use of empirical data to generate theoretical future projections in the form of median time to extinction and probability of extinction. In turn, PVAs can inform and aid the development of conservation, recovery, and management plans. Pitcher's thistle (Cirsium pitcheri) is a dune endemic that exhibited metapopulation dynamics. We projected viability of three natural and two restored populations with demographic data spanning 15–23 years to determine the degree the addition of reintroduced population affects metapopulation viability. The models were validated by comparing observed and projected abundances and adjusting parameters associated with demographic and environmental stochasticity to improve model performance. Our chosen model correctly predicted yearly population abundance for 60% of the population-years. Using that model, 50-year projections showed that the addition of reintroductions increases metapopulation viability. The reintroduction that simulated population performance in early-successional habitats had the maximum benefit. In situ enhancements of existing populations proved to be equally effective. This study shows that restorations can facilitate and improve metapopulation viability of species dependent on metapopulation dynamics for survival with long-term persistence of C. pitcheri in Indiana likely to depend on continued active management.

Anomalous finite-size effects in the Battle of the Sexes

NASA Astrophysics Data System (ADS)

Cremer, J.; Reichenbach, T.; Frey, E.

2008-06-01

The Battle of the Sexes describes asymmetric conflicts in mating behavior of males and females. Males can be philanderer or faithful, while females are either fast or coy, leading to a cyclic dynamics. The adjusted replicator equation predicts stable coexistence of all four strategies. In this situation, we consider the effects of fluctuations stemming from a finite population size. We show that they unavoidably lead to extinction of two strategies in the population. However, the typical time until extinction occurs strongly prolongs with increasing system size. In the emerging time window, a quasi-stationary probability distribution forms that is anomalously flat in the vicinity of the coexistence state. This behavior originates in a vanishing linear deterministic drift near the fixed point. We provide numerical data as well as an analytical approach to the mean extinction time and the quasi-stationary probability distribution.

Genetic isolation of a now extinct population of bottlenose dolphins (Tursiops truncatus)

PubMed Central

Nichols, Courtney; Herman, Jerry; Gaggiotti, Oscar E; Dobney, Keith M; Parsons, Kim; Hoelzel, A. Rus

2007-01-01

A number of dolphin species, though highly mobile, show genetic structure among parapatric and sometimes sympatric populations. However, little is known about the temporal patterns of population structure for these species. Here, we apply Bayesian inference and data from ancient DNA to assess the structure and dynamics of bottlenose dolphin (Tursiops truncatus) populations in the coastal waters of the UK. We show that regional population structure in UK waters is consistent with earlier studies suggesting local habitat dependence for this species in the Mediterranean Sea and North Atlantic. One genetically differentiated UK population went extinct at least 100 years ago and has not been replaced. The data indicate that this was a local extinction, and not a case of historical range shift or contraction. One possible interpretation is a declining metapopulation and conservation need for this species in the UK. PMID:17456457

Flip-chip integrated silicon Mach-Zehnder modulator with a 28nm fully depleted silicon-on-insulator CMOS driver.

PubMed

Yong, Zheng; Shopov, Stefan; Mikkelsen, Jared C; Mallard, Robert; Mak, Jason C C; Voinigescu, Sorin P; Poon, Joyce K S

2017-03-20

We present a silicon electro-optic transmitter consisting of a 28nm ultra-thin body and buried oxide fully depleted silicon-on-insulator (UTBB FD-SOI) CMOS driver flip-chip integrated onto a Mach-Zehnder modulator. The Mach-Zehnder silicon optical modulator was optimized to have a 3dB bandwidth of around 25 GHz at -1V bias and a 50 Ω impedance. The UTBB FD-SOI CMOS driver provided a large output voltage swing around 5 V_pp to enable a high dynamic extinction ratio and a low device insertion loss. At 44 Gbps, the transmitter achieved a high extinction ratio of 6.4 dB at the modulator quadrature operation point. This result shows open eye diagrams at the highest bit rates and with the largest extinction ratios for silicon electro-optic transmitter using a CMOS driver.

Species survival emerge from rare events of individual migration

NASA Astrophysics Data System (ADS)

Zelnik, Yuval R.; Solomon, Sorin; Yaari, Gur

2015-01-01

Ecosystems greatly vary in their species composition and interactions, yet they all show remarkable resilience to external influences. Recent experiments have highlighted the significant effects of spatial structure and connectivity on the extinction and survival of species. It has also been emphasized lately that in order to study extinction dynamics reliably, it is essential to incorporate stochasticity, and in particular the discrete nature of populations, into the model. Accordingly, we applied a bottom-up modeling approach that includes both spatial features and stochastic interactions to study survival mechanisms of species. Using the simplest spatial extension of the Lotka-Volterra predator-prey model with competition, subject to demographic and environmental noise, we were able to systematically study emergent properties of this rich system. By scanning the relevant parameter space, we show that both survival and extinction processes often result from a combination of habitat fragmentation and individual rare events of recolonization.

A discrete Markov metapopulation model for persistence and extinction of species.

PubMed

Thompson, Colin J; Shtilerman, Elad; Stone, Lewi

2016-09-07

A simple discrete generation Markov metapopulation model is formulated for studying the persistence and extinction dynamics of a species in a given region which is divided into a large number of sites or patches. Assuming a linear site occupancy probability from one generation to the next we obtain exact expressions for the time evolution of the expected number of occupied sites and the mean-time to extinction (MTE). Under quite general conditions we show that the MTE, to leading order, is proportional to the logarithm of the initial number of occupied sites and in precise agreement with similar expressions for continuous time-dependent stochastic models. Our key contribution is a novel application of generating function techniques and simple asymptotic methods to obtain a second order asymptotic expression for the MTE which is extremely accurate over the entire range of model parameter values. Copyright © 2016 Elsevier Ltd. All rights reserved.

Extinction ratio enhancement of SOA-based delayed-interference signal converter using detuned filtering

NASA Astrophysics Data System (ADS)

Zhang, B.; Kumar, S.; Yan, L.-S.; Willner, A. E.

2007-12-01

We demonstrate experimentally >3 dB extinction ratio improvement at the output of SOA-based delayed-interference signal converter (DISC) using optical off-centered filtering. Through careful modeling of the carrier and the phase dynamics, we explain in detail the origin of sub-pulses in the wavelength converted output, with an emphasis on the time-resolved frequency chirping of the output signal. Through our simulations we conclude that the sub-pulses and the main-pulses are oppositely chirped, which is also verified experimentally by analyzing the output with a chirp form analyzer. We propose and demonstrate an optical off-center filtering technique which effectively suppresses these sub-pulses. The effects of filter detuning and phase bias adjustment in the delayed-interferometer are experimentally characterized and optimized, leading to a >3 dB extinction ratio enhancement of the output signal.

Species survival emerge from rare events of individual migration.

PubMed

Zelnik, Yuval R; Solomon, Sorin; Yaari, Gur

2015-01-19

Ecosystems greatly vary in their species composition and interactions, yet they all show remarkable resilience to external influences. Recent experiments have highlighted the significant effects of spatial structure and connectivity on the extinction and survival of species. It has also been emphasized lately that in order to study extinction dynamics reliably, it is essential to incorporate stochasticity, and in particular the discrete nature of populations, into the model. Accordingly, we applied a bottom-up modeling approach that includes both spatial features and stochastic interactions to study survival mechanisms of species. Using the simplest spatial extension of the Lotka-Volterra predator-prey model with competition, subject to demographic and environmental noise, we were able to systematically study emergent properties of this rich system. By scanning the relevant parameter space, we show that both survival and extinction processes often result from a combination of habitat fragmentation and individual rare events of recolonization.

Unsteady Extinction of Opposed Jet Ethylene/Methane HIFiRE Surrogate Fuel Mixtures vs Air

NASA Technical Reports Server (NTRS)

Vaden, Sarah N.; Debes, Rachel L.; Lash, E. Lara; Burk, Rachel S.; Boyd, C. Merritt; Wilson, Lloyd G.; Pellett, Gerald L.

2009-01-01

A unique idealized study of the subject fuel vs. air systems was conducted using an Oscillatory-input Opposed Jet Burner (OOJB) system and a newly refined analysis. Extensive dynamic-extinction measurements were obtained on unanchored (free-floating) laminar Counter Flow Diffusion Flames (CFDFs) at 1-atm, stabilized by steady input velocities (e.g., U(sub air)) and perturbed by superimposed in-phase sinusoidal velocity inputs at fuel and air nozzle exits. Ethylene (C2H4) and methane (CH4), and intermediate 64/36 and 15/85 molar percent mixtures were studied. The latter gaseous surrogates were chosen earlier to mimic ignition and respective steady Flame Strengths (FS = U(sub air)) of vaporized and cracked, and un-cracked, JP-7 "like" kerosene for a Hypersonic International Flight Research Experimentation (HIFiRE) scramjet. For steady idealized flameholding, the 100% C2H4 flame is respectively approx. 1.3 and approx.2.7 times stronger than a 64/36 mix and CH4; but is still 12.0 times weaker than a 100% H2-air flame. Limited Hot-Wire (HW) measurements of velocity oscillations at convergent-nozzle exits, and more extensive Probe Microphone (PM) measurements of acoustic pressures, were used to normalize Dynamic FSs, which decayed linearly with pk/pk U(sub air) (velocity magnitude, HW), and also pk/pk P (pressure magnitude, PM). Thus Dynamic Flame Weakening (DFW) is defined as % decrease in FS per Pascal of pk/pk P oscillation, namely, DFW = -100 d(U(sub air)/U(sub air),0Hz)/d(pkpk P). Key findings are: (1) Ethylene flames are uniquely strong and resilient to extinction by oscillating inflows below 150 Hz; (2) Methane flames are uniquely weak; (3) Ethylene / methane surrogate flames are disproportionately strong with respect to ethylene content; and (4) Flame weakening is consistent with limited published results on forced unsteady CFDFs. Thus from 0 to approx. 10 Hz and slightly higher, lagging diffusive responses of key species led to progressive phase lags (relative to inputs) in the oscillating flames, and caused maximum weakening. At 20 to 150 Hz, diffusion-rate-limited effects diminished, causing flames to "regain strengnth," and eventually become completely insensitive beyond 300 Hz. Detailed mechanistic understanding is needed. Overall, ethylene flames are remarkably resilient to dynamic extinction by oscillating inflows. They are the strongest, with the notable exception of H2. For HIFiRE tests, the 64%/36% surrogate disproportionally retains the high dynamic FS of ethylene, so the potential for loss of scramjet flameholding (flameout) due to low frequency oscillations is significantly mitigated.

Counting motifs in dynamic networks.

PubMed

Mukherjee, Kingshuk; Hasan, Md Mahmudul; Boucher, Christina; Kahveci, Tamer

2018-04-11

A network motif is a sub-network that occurs frequently in a given network. Detection of such motifs is important since they uncover functions and local properties of the given biological network. Finding motifs is however a computationally challenging task as it requires solving the costly subgraph isomorphism problem. Moreover, the topology of biological networks change over time. These changing networks are called dynamic biological networks. As the network evolves, frequency of each motif in the network also changes. Computing the frequency of a given motif from scratch in a dynamic network as the network topology evolves is infeasible, particularly for large and fast evolving networks. In this article, we design and develop a scalable method for counting the number of motifs in a dynamic biological network. Our method incrementally updates the frequency of each motif as the underlying network's topology evolves. Our experiments demonstrate that our method can update the frequency of each motif in orders of magnitude faster than counting the motif embeddings every time the network changes. If the network evolves more frequently, the margin with which our method outperforms the existing static methods, increases. We evaluated our method extensively using synthetic and real datasets, and show that our method is highly accurate(≥ 96%) and that it can be scaled to large dense networks. The results on real data demonstrate the utility of our method in revealing interesting insights on the evolution of biological processes.

Some mechanistic requirements for major transitions

PubMed Central

2016-01-01

Major transitions in nature and human society are accompanied by a substantial change towards higher complexity in the core of the evolving system. New features are established, novel hierarchies emerge, new regulatory mechanisms are required and so on. An obvious way to achieve higher complexity is integration of autonomous elements into new organized systems whereby the previously independent units give up their autonomy at least in part. In this contribution, we reconsider the more than 40 years old hypercycle model and analyse it by the tools of stochastic chemical kinetics. An open system is implemented in the form of a flow reactor. The formation of new dynamically organized units through integration of competitors is identified with transcritical bifurcations. In the stochastic model, the fully organized state is quasi-stationary whereas the unorganized state corresponds to a population with natural selection. The stability of the organized state depends strongly on the number of individual subspecies, n, that have to be integrated: two and three classes of individuals, and , readily form quasi-stationary states. The four-membered deterministic dynamical system, , is stable but in the stochastic approach self-enhancing fluctuations drive it into extinction. In systems with five and more classes of individuals, , the state of cooperation is unstable and the solutions of the deterministic ODEs exhibit large amplitude oscillations. In the stochastic system self-enhancing fluctuations lead to extinction as observed with . Interestingly, cooperative systems in nature are commonly two-membered as shown by numerous examples of binary symbiosis. A few cases of symbiosis of three partners, called three-way symbiosis, have been found and were analysed within the past decade. Four-way symbiosis is rather rare but was reported to occur in fungus-growing ants. The model reported here can be used to illustrate the interplay between competition and cooperation whereby we obtain a hint on the role that resources play in major transitions. Abundance of resources seems to be an indispensable prerequisite of radical innovation that apparently needs substantial investments. Economists often claim that scarcity is driving innovation. Our model sheds some light on this apparent contradiction. In a nutshell, the answer is: scarcity drives optimization and increase in efficiency but abundance is required for radical novelty and the development of new features. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431517

Floral biology and ovule and seed ontogeny of Nymphaea thermarum, a water lily at the brink of extinction with potential as a model system for basal angiosperms

PubMed Central

Povilus, Rebecca A.; Losada, Juan M.; Friedman, William E.

2015-01-01

Background and Aims Nymphaea thermarum is a member of the Nymphaeales, of one of the most ancient lineages of flowering plants. This species was only recently described and then declared extinct in the wild, so little is known about its reproductive biology. In general, the complete ontogeny of ovules and seeds is not well documented among species of Nymphaea and has never been studied in the subgenus Brachyceras, the clade to which N. thermarum belongs. Methods Flowers and fruits were processed for brightfield, epifluorescence and confocal microscopy. Flower morphology, with emphasis on the timing of male and female functions, was correlated with key developmental stages of the ovule and the female gametophyte. Development of the seed tissues and dynamics of polysaccharide reserves in the endosperm, perisperm and embryo were examined. Key Results Pollen release in N. thermarum starts before the flower opens. Cell walls of the micropylar nucellus show layering of callose and cellulose in a manner reminiscent of transfer cell wall patterning. Endosperm development is ab initio cellular, with micropylar and chalazal domains that embark on distinct developmental trajectories. The surrounding maternal perisperm occupies the majority of seed volume and accumulates starch centrifugally. In mature seeds, a minute but fully developed embryo is surrounded by a single, persistent layer of endosperm. Conclusions Early male and female function indicate that N. thermarum is predisposed towards self-pollination, a phenomenon that is likely to have evolved multiple times within Nymphaea. While formation of distinct micropylar and chalazal developmental domains in the endosperm, along with a copious perisperm, characterize the seeds of most members of the Nymphaeales, seed ontogenies vary between and among the constituent families. Floral biology, life history traits and small genome size make N. thermarum uniquely promising as an early-diverging angiosperm model system for genetic and molecular studies. PMID:25497514

Management of percids in Lake Erie, North America

USGS Publications Warehouse

Hatch, Richard W.; Nepszy, Stephen J.; Rawson, Michael R.; van Densen, W.L.T.; Steinmetz, B.; Hughes, R.H.

1990-01-01

Lake Erie's fish populations and their habitats have undergone very substantial changes since 1945. Of the four percid forms originally present, the blue pike (Stizostedion vitreum glaucum) is presumed extinct, and the sauger (S. canadense) was commercially extinct by the 1950's. The walleye (S. v. vitreum) has remained stable in eastern Lake Erie but the highly productive stock of the western basin collapsed in the 1960's. Closure of the walleye fishery from 1970 to 1973, necessitated by mercury contamination, provided an opportunity for the development of an international management plan for restoration of the stock. An inter-agency Scientific Protocol Committee evaluated walleye dynamics and recommended management by quota beginning in 1976. Although quotas have been exceeded several times, the walleye stock responded well to limited exploitation, steadily increased, and expanded its range. Landings of the yellow perch (Perca flavescens) increased during the 1950's, but a steady decline in abundance, beginning in the early 1970's led to the formation in 1980 of another international inter-agency task group to recommend a basis for quota management. The short-term management recommendation, reported and accepted in 1986, was to reduce fishing effort by 20% by 1990. Both management schemes evolved when the resource agencies of the five jurisdictions (New York, Pennsylvania, Ohio, Michigan, and Ontario), in the two nations surrounding Lake Erie, perceived a need for the increased and improved management of a shared resource. They sought an international forum in which to develop strategies, appointed inter-agency scientific task groups to develop a basis for management recommendations, and adopted a quota management scheme. Each jurisdiction is responsible for the enforcement and allocation of its portion of the quota between user groups. Reports of catch, effort, and biological observations on stock performance are submitted annually to a standing technical committee charged with updating quotas.

Time to Evolve? Potential Evolutionary Responses of Fraser River Sockeye Salmon to Climate Change and Effects on Persistence

PubMed Central

Reed, Thomas E.; Schindler, Daniel E.; Hague, Merran J.; Patterson, David A.; Meir, Eli; Waples, Robin S.; Hinch, Scott G.

2011-01-01

Evolutionary adaptation affects demographic resilience to climate change but few studies have attempted to project changes in selective pressures or quantify impacts of trait responses on population dynamics and extinction risk. We used a novel individual-based model to explore potential evolutionary changes in migration timing and the consequences for population persistence in sockeye salmon Oncorhynchus nerka in the Fraser River, Canada, under scenarios of future climate warming. Adult sockeye salmon are highly sensitive to increases in water temperature during their arduous upriver migration, raising concerns about the fate of these ecologically, culturally, and commercially important fish in a warmer future. Our results suggest that evolution of upriver migration timing could allow these salmon to avoid increasingly frequent stressful temperatures, with the odds of population persistence increasing in proportion to the trait heritability and phenotypic variance. With a simulated 2°C increase in average summer river temperatures by 2100, adult migration timing from the ocean to the river advanced by ∼10 days when the heritability was 0.5, while the risk of quasi-extinction was only 17% of that faced by populations with zero evolutionary potential (i.e., heritability fixed at zero). The rates of evolution required to maintain persistence under simulated scenarios of moderate to rapid warming are plausible based on estimated heritabilities and rates of microevolution of timing traits in salmon and related species, although further empirical work is required to assess potential genetic and ecophysiological constraints on phenological adaptation. These results highlight the benefits to salmon management of maintaining evolutionary potential within populations, in addition to conserving key habitats and minimizing additional stressors where possible, as a means to build resilience to ongoing climate change. More generally, they demonstrate the importance and feasibility of considering evolutionary processes, in addition to ecology and demography, when projecting population responses to environmental change. PMID:21738573

Quantumness-generating capability of quantum dynamics

NASA Astrophysics Data System (ADS)

Li, Nan; Luo, Shunlong; Mao, Yuanyuan

2018-04-01

We study quantumness-generating capability of quantum dynamics, where quantumness refers to the noncommutativity between the initial state and the evolving state. In terms of the commutator of the square roots of the initial state and the evolving state, we define a measure to quantify the quantumness-generating capability of quantum dynamics with respect to initial states. Quantumness-generating capability is absent in classical dynamics and hence is a fundamental characteristic of quantum dynamics. For qubit systems, we present an analytical form for this measure, by virtue of which we analyze several prototypical dynamics such as unitary dynamics, phase damping dynamics, amplitude damping dynamics, and random unitary dynamics (Pauli channels). Necessary and sufficient conditions for the monotonicity of quantumness-generating capability are also identified. Finally, we compare these conditions for the monotonicity of quantumness-generating capability with those for various Markovianities and illustrate that quantumness-generating capability and quantum Markovianity are closely related, although they capture different aspects of quantum dynamics.

Droplet Combustion Experiments Aboard the International Space Station

NASA Astrophysics Data System (ADS)

Dietrich, Daniel L.; Nayagam, Vedha; Hicks, Michael C.; Ferkul, Paul V.; Dryer, Frederick L.; Farouk, Tanvir; Shaw, Benjamin D.; Suh, Hyun Kyu; Choi, Mun Y.; Liu, Yu Cheng; Avedisian, C. Thomas; Williams, Forman A.

2014-10-01

This paper summarizes the first results from isolated droplet combustion experiments performed on the International Space Station (ISS). The long durations of microgravity provided in the ISS enable the measurement of droplet and flame histories over an unprecedented range of conditions. The first experiments were with heptane and methanol as fuels, initial droplet droplet diameters between 1.5 and 5.0 m m, ambient oxygen mole fractions between 0.1 and 0.4, ambient pressures between 0.7 and 3.0 a t m and ambient environments containing oxygen and nitrogen diluted with both carbon dioxide and helium. The experiments show both radiative and diffusive extinction. For both fuels, the flames exhibited pre-extinction flame oscillations during radiative extinction with a frequency of approximately 1 H z. The results revealed that as the ambient oxygen mole fraction was reduced, the diffusive-extinction droplet diameter increased and the radiative-extinction droplet diameter decreased. In between these two limiting extinction conditions, quasi-steady combustion was observed. Another important measurement that is related to spacecraft fire safety is the limiting oxygen index (LOI), the oxygen concentration below which quasi-steady combustion cannot be supported. This is also the ambient oxygen mole fraction for which the radiative and diffusive extinction diameters become equal. For oxygen/nitrogen mixtures, the LOI is 0.12 and 0.15 for methanol and heptane, respectively. The LOI increases to approximately 0.14 (0.14 O 2/0.56 N 2/0.30 C O 2) and 0.17 (0.17 O 2/0.63 N 2/0.20 C O 2) for methanol and heptane, respectively, for ambient environments that simulated dispersing an inert-gas suppressant (carbon dioxide) into a nominally air (1.0 a t m) ambient environment. The LOI is approximately 0.14 and 0.15 for methanol and heptane, respectively, when helium is dispersed into air at 1 atm. The experiments also showed unique burning behavior for large heptane droplets. After the visible hot flame radiatively extinguished around a large heptane droplet, the droplet continued to burn with a cool flame. This phenomena was observed repeatably over a wide range of ambient conditions. These cool flames were invisible to the experiment imaging system but their behavior was inferred by the sustained quasi-steady burning after visible flame extinction. Verification of this new burning regime was established by both theoretical and numerical analysis of the experimental results. These innovative experiments have provided a wealth of new data for improving the understanding of droplet combustion and related aspects of fire safety, as well as offering important measurements that can be used to test sophisticated evolving computational models and theories of droplet combustion.

Convergence in Thunniform Anatomy in Lamnid Sharks and Jurassic Ichthyosaurs.

PubMed

Lingham-Soliar, Theagarten

2016-12-01

Among extinct ichthyosaurs the Jurassic forms Ichthyosaurus and Stenopterygius share a number of anatomical specializations with lamnid sharks, characterized in the white shark, Carcharodon carcharias These features allow their inclusion within the mode of high-speed thunniform swimming to which only two other equally distinctive phylogenetic groups belong, tuna and dolphins-a striking testaments to evolutionary convergence. Jurassic ichthyosaurs evolved from reptiles that had returned to the sea (secondarily adapted) about 250 million years ago (MYA) while lamnid sharks evolved about 50 MYA from early cartilaginous fishes (originating ca. 400 MYA). Their shared independently evolved anatomical characteristics are discussed. These include a deep tear-drop body shape that helped initially define members as thunniform swimmers. Later, other critical structural characteristics were discovered such as the crossed-fiber architecture of the skin, high-speed adapted dorsal and caudal fins, a caudal peduncle and series of ligaments to enable transmission of power from the musculature located anteriorly to the caudal fin. Both groups also share a similar chemistry of the dermal fibers, i.e., the scleroprotein collagen. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

The Influence of Agroforestry and Other Land-Use Types on the Persistence of a Sumatran Tiger ( Panthera tigris sumatrae) Population: An Individual-Based Model Approach

NASA Astrophysics Data System (ADS)

Imron, Muhammad Ali; Herzog, Sven; Berger, Uta

2011-08-01

The importance of preserving both protected areas and their surrounding landscapes as one of the major conservation strategies for tigers has received attention over recent decades. However, the mechanism of how land-use surrounding protected areas affects the dynamics of tiger populations is poorly understood. We developed Panthera Population Persistence (PPP)—an individual-based model—to investigate the potential mechanism of the Sumatran tiger population dynamics in a protected area and under different land-use scenarios surrounding the reserve. We tested three main landscape compositions (single, combined and real land-uses of Tesso-Nilo National Park and its surrounding area) on the probability of and time to extinction of the Sumatran tiger over 20 years in Central Sumatra. The model successfully explains the mechanisms behind the population response of tigers under different habitat landscape compositions. Feeding and mating behaviours of tigers are key factors, which determined population persistence in a heterogeneous landscape. All single land-use scenarios resulted in tiger extinction but had a different probability of extinction within 20 years. If tropical forest was combined with other land-use types, the probability of extinction was smaller. The presence of agroforesty and logging concessions adjacent to protected areas encouraged the survival of tiger populations. However, with the real land-use scenario of Tesso-Nilo National Park, tigers could not survive for more than 10 years. Promoting the practice of agroforestry systems surrounding the park is probably the most reasonable way to steer land-use surrounding the Tesso-Nilo National Park to support tiger conservation.

The origin of conodonts and of vertebrate mineralized skeletons

USGS Publications Warehouse

Murdock, Duncan J.E.; Dong, Xi-Ping; Repetski, John E.; Marone, Federica; Stampanoni, Marco; Donoghue, Philip C.J.

2013-01-01

Conodonts are an extinct group of jawless vertebrates whose tooth-like elements are the earliest instance of a mineralized skeleton in the vertebrate lineage, inspiring the ‘inside-out’ hypothesis that teeth evolved independently of the vertebrate dermal skeleton and before the origin of jaws. However, these propositions have been based on evidence from derived euconodonts. Here we test hypotheses of a paraconodont ancestry of euconodonts using synchrotron radiation X-ray tomographic microscopy to characterize and compare the microstructure of morphologically similar euconodont and paraconodont elements. Paraconodonts exhibit a range of grades of structural differentiation, including tissues and a pattern of growth common to euconodont basal bodies. The different grades of structural differentiation exhibited by paraconodonts demonstrate the stepwise acquisition of euconodont characters, resolving debate over the relationship between these two groups. By implication, the putative homology of euconodont crown tissue and vertebrate enamel must be rejected as these tissues have evolved independently and convergently. Thus, the precise ontogenetic, structural and topological similarities between conodont elements and vertebrate odontodes appear to be a remarkable instance of convergence. The last common ancestor of conodonts and jawed vertebrates probably lacked mineralized skeletal tissues. The hypothesis that teeth evolved before jaws and the inside-out hypothesis of dental evolution must be rejected; teeth seem to have evolved through the extension of odontogenic competence from the external dermis to internal epithelium soon after the origin of jaws.

The relationship between species detection probability and local extinction probability

USGS Publications Warehouse

Alpizar-Jara, R.; Nichols, J.D.; Hines, J.E.; Sauer, J.R.; Pollock, K.H.; Rosenberry, C.S.

2004-01-01

In community-level ecological studies, generally not all species present in sampled areas are detected. Many authors have proposed the use of estimation methods that allow detection probabilities that are < 1 and that are heterogeneous among species. These methods can also be used to estimate community-dynamic parameters such as species local extinction probability and turnover rates (Nichols et al. Ecol Appl 8:1213-1225; Conserv Biol 12:1390-1398). Here, we present an ad hoc approach to estimating community-level vital rates in the presence of joint heterogeneity of detection probabilities and vital rates. The method consists of partitioning the number of species into two groups using the detection frequencies and then estimating vital rates (e.g., local extinction probabilities) for each group. Estimators from each group are combined in a weighted estimator of vital rates that accounts for the effect of heterogeneity. Using data from the North American Breeding Bird Survey, we computed such estimates and tested the hypothesis that detection probabilities and local extinction probabilities were negatively related. Our analyses support the hypothesis that species detection probability covaries negatively with local probability of extinction and turnover rates. A simulation study was conducted to assess the performance of vital parameter estimators as well as other estimators relevant to questions about heterogeneity, such as coefficient of variation of detection probabilities and proportion of species in each group. Both the weighted estimator suggested in this paper and the original unweighted estimator for local extinction probability performed fairly well and provided no basis for preferring one to the other.

The role of prestimulus activity in visual extinction☆

PubMed Central

Urner, Maren; Sarri, Margarita; Grahn, Jessica; Manly, Tom; Rees, Geraint; Friston, Karl

2013-01-01

Patients with visual extinction following right-hemisphere damage sometimes see and sometimes miss stimuli in the left visual field, particularly when stimuli are presented simultaneously to both visual fields. Awareness of left visual field stimuli is associated with increased activity in bilateral parietal and frontal cortex. However, it is unknown why patients see or miss these stimuli. Previous neuroimaging studies in healthy adults show that prestimulus activity biases perceptual decisions, and biases in visual perception can be attributed to fluctuations in prestimulus activity in task relevant brain regions. Here, we used functional MRI to investigate whether prestimulus activity affected perception in the context of visual extinction following stroke. We measured prestimulus activity in stimulus-responsive cortical areas during an extinction paradigm in a patient with unilateral right parietal damage and visual extinction. This allowed us to compare prestimulus activity on physically identical bilateral trials that either did or did not lead to visual extinction. We found significantly increased activity prior to stimulus presentation in two areas that were also activated by visual stimulation: the left calcarine sulcus and right occipital inferior cortex. Using dynamic causal modelling (DCM) we found that both these differences in prestimulus activity and stimulus evoked responses could be explained by enhanced effective connectivity within and between visual areas, prior to stimulus presentation. Thus, we provide evidence for the idea that differences in ongoing neural activity in visually responsive areas prior to stimulus onset affect awareness in visual extinction, and that these differences are mediated by fluctuations in extrinsic and intrinsic connectivity. PMID:23680398

The Arches Cluster Out to its Tidal Radius: Dynamical Mass Segregation and the Effect of the Extinction Law on the - Lar Mass Function

NASA Astrophysics Data System (ADS)

Habibi, Maryam; Stolte, Andrea; Brandner, Wolfgang; Hussman, Benjamin

2013-07-01

The Galactic Center is the most active site of star formation in the Milky Way Galaxy, where particularly high-mass stars have formed very recently and are still forming today. However, since we are looking at the Galactic Center through the Galactic disk, knowledge of extinction is crucial to study this region. The Arches cluster is a young, massive starburst cluster near the Galactic Center. We observed the Arches cluster out to its tidal radius using Ks-band imaging obtained with NAOS/CONICA at the VLT combined with Subaro/Cisco J-band data to gain a full understanding of the cluster mass distribution. We show that the determination of the mass of the most massive star in the Arches cluster, which had been used in previous studies to establish an upper-mass limit for the star formation process in the Milky Way, strongly depends on the assumed slope of the extinction law. Assuming the two regimes of widely used infrared extinction laws, we show that the difference can reach up to 30% for individually derived stellar masses and ∆AKs˜1 magnitude in acquired Ks-band extinction, while the present mass function slope changes by ˜0.17 dex. The present-day mass function slope derived assuming the Nishiyama et al. (2009) extinction law increases from a flat slope of α-Nishi = 1.50 ± 0.35 in the core (r<0.2 pc) to α-Nishi = 2.21±0.27 in the intermediate annulus (0.2

Modeling ecological traps for the control of feral pigs

PubMed Central

Dexter, Nick; McLeod, Steven R

2015-01-01

Ecological traps are habitat sinks that are preferred by dispersing animals but have higher mortality or reduced fecundity compared to source habitats. Theory suggests that if mortality rates are sufficiently high, then ecological traps can result in extinction. An ecological trap may be created when pest animals are controlled in one area, but not in another area of equal habitat quality, and when there is density-dependent immigration from the high-density uncontrolled area to the low-density controlled area. We used a logistic population model to explore how varying the proportion of habitat controlled, control mortality rate, and strength of density-dependent immigration for feral pigs could affect the long-term population abundance and time to extinction. Increasing control mortality, the proportion of habitat controlled and the strength of density-dependent immigration decreased abundance both within and outside the area controlled. At higher levels of these parameters, extinction was achieved for feral pigs. We extended the analysis with a more complex stochastic, interactive model of feral pig dynamics in the Australian rangelands to examine how the same variables as the logistic model affected long-term abundance in the controlled and uncontrolled area and time to extinction. Compared to the logistic model of feral pig dynamics, the stochastic interactive model predicted lower abundances and extinction at lower control mortalities and proportions of habitat controlled. To improve the realism of the stochastic interactive model, we substituted fixed mortality rates with a density-dependent control mortality function, empirically derived from helicopter shooting exercises in Australia. Compared to the stochastic interactive model with fixed mortality rates, the model with the density-dependent control mortality function did not predict as substantial decline in abundance in controlled or uncontrolled areas or extinction for any combination of variables. These models demonstrate that pest eradication is theoretically possible without the pest being controlled throughout its range because of density-dependent immigration into the area controlled. The stronger the density-dependent immigration, the better the overall control in controlled and uncontrolled habitat combined. However, the stronger the density-dependent immigration, the poorer the control in the area controlled. For feral pigs, incorporating environmental stochasticity improves the prospects for eradication, but adding a realistic density-dependent control function eliminates these prospects. PMID:26045954

The evolution of resource adaptation: how generalist and specialist consumers evolve.

PubMed

Ma, Junling; Levin, Simon A

2006-07-01

Why and how specialist and generalist strategies evolve are important questions in evolutionary ecology. In this paper, with the method of adaptive dynamics and evolutionary branching, we identify conditions that select for specialist and generalist strategies. Generally, generalist strategies evolve if there is a switching benefit; specialists evolve if there is a switching cost. If the switching cost is large, specialists always evolve. If the switching cost is small, even though the consumer will first evolve toward a generalist strategy, it will eventually branch into two specialists.

The influence of space and time on the evolution of altruistic defence: the case of ant slave rebellion.

PubMed

Metzler, D; Jordan, F; Pamminger, T; Foitzik, S

2016-05-01

How can antiparasite defence traits evolve even if they do not directly benefit their carriers? An example of such an indirect defence is rebellion of enslaved Temnothorax longispinosus ant workers against their social parasite Temnothorax americanus, a slavemaking ant. Ant slaves have been observed to kill their oppressors' offspring, a behaviour from which the sterile slaves cannot profit directly. Parasite brood killing could, however, reduce raiding pressure on related host colonies nearby. We analyse with extensive computer simulations for the Temnothorax slavemaker system under what conditions a hypothetical rebel allele could invade a host population, and in particular, how host-parasite dynamics and population structure influence the rebel allele's success. Exploring a wide range of model parameters, we only found a small number of parameter combinations for which kin selection or multilevel selection could allow a slave rebellion allele to spread in the host population. Furthermore, we did not detect any cases in which the reduction of raiding pressure in the close vicinity of the slavemaker nest would substantially contribute to the inclusive fitness of rebels. This suggests that slave rebellion is not costly and perhaps a side-effect of some other beneficial trait. In some of our simulations, however, even a costly rebellion allele could spread in the population. This was possible when host-parasite interactions led to a metapopulation dynamic with frequent local extinctions and recolonizations of demes by the offspring of few immigrants. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Extreme Telomere Length Dimorphism in the Tasmanian Devil and Related Marsupials Suggests Parental Control of Telomere Length

PubMed Central

Bender, Hannah S.; Murchison, Elizabeth P.; Pickett, Hilda A.; Deakin, Janine E.; Strong, Margaret A.; Conlan, Carly; McMillan, Daniel A.; Neumann, Axel A.; Greider, Carol W.; Hannon, Gregory J.; Reddel, Roger R.; Graves, Jennifer A. Marshall.

2012-01-01

Telomeres, specialised structures that protect chromosome ends, play a critical role in preserving chromosome integrity. Telomere dynamics in the Tasmanian devil (Sarcophilus harrisii) are of particular interest in light of the emergence of devil facial tumour disease (DFTD), a transmissible malignancy that causes rapid mortality and threatens the species with extinction. We used fluorescent in situ hybridisation to investigate telomere length in DFTD cells, in healthy Tasmanian devils and in four closely related marsupial species. Here we report that animals in the Order Dasyuromorphia have chromosomes characterised by striking telomere length dimorphism between homologues. Findings in sex chromosomes suggest that telomere length dimorphism may be regulated by events in the parental germlines. Long telomeres on the Y chromosome imply that telomere lengthening occurs during spermatogenesis, whereas telomere diminution occurs during oogenesis. Although found in several somatic cell tissue types, telomere length dimorphism was not found in DFTD cancer cells, which are characterised by uniformly short telomeres. This is, to our knowledge, the first report of naturally occurring telomere length dimorphism in any species and suggests a novel strategy of telomere length control. Comparative studies in five distantly related marsupials and a monotreme indicate that telomere dimorphism evolved at least 50 million years ago. PMID:23049977

The origin and evolution of coral species richness in a marine biodiversity hotspot.

PubMed

Huang, Danwei; Goldberg, Emma E; Chou, Loke Ming; Roy, Kaustuv

2018-02-01

The Coral Triangle (CT) region of the Indo-Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here, we use a time-calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model-based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the CT are lower than in surrounding regions, a result inconsistent with the long-standing center of origin hypothesis. Furthermore, endemism of coral species in the CT is low, and the CT endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the CT is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the CT requires protecting not just reefs within the hotspot, but also those in the surrounding areas. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Fixation probabilities of evolutionary coordination games on two coupled populations

NASA Astrophysics Data System (ADS)

Zhang, Liye; Ying, Limin; Zhou, Jie; Guan, Shuguang; Zou, Yong

2016-09-01

Evolutionary forces resulted from competitions between different populations are common, which change the evolutionary behavior of a single population. In an isolated population of coordination games of two strategies (e.g., s1 and s2), the previous studies focused on determining the fixation probability that the system is occupied by only one strategy (s1) and their expectation times, given an initial mixture of two strategies. In this work, we propose a model of two interdependent populations, disclosing the effects of the interaction strength on fixation probabilities. In the well-mixing limit, a detailed linear stability analysis is performed, which allows us to find and to classify the different equilibria, yielding a clear picture of the bifurcation patterns in phase space. We demonstrate that the interactions between populations crucially alter the dynamic behavior. More specifically, if the coupling strength is larger than some threshold value, the critical initial density of one strategy (s1) that corresponds to fixation is significantly delayed. Instead, the two populations evolve to the opposite state of all (s2) strategy, which are in favor of the red queen hypothesis. We delineate the extinction time of strategy (s1) explicitly, which is an exponential form. These results are validated by systematic numerical simulations.

Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages

PubMed Central

Santos, Juan C; Coloma, Luis A; Summers, Kyle; Caldwell, Janalee P; Ree, Richard; Cannatella, David C

2009-01-01

The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity. However, determinants of Neotropical biodiversity (i.e., vicariance, dispersals, extinctions, and radiations) earlier than the Quaternary are largely unstudied. Using a novel method of ancestral area reconstruction and relaxed Bayesian clock analyses, we reconstructed the biogeography of the poison frog clade (Dendrobatidae). We rejected an Amazonian center-of-origin in favor of a complex connectivity model expanding over the Neotropics. We inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. We found three episodes of lineage dispersal with two interleaved periods of vicariant events between South and Central America. During the late Miocene, Amazonian, and Central American-Chocoan lineages significantly increased their diversity compared to the Andean and Guianan-Venezuelan-Brazilian Shield counterparts. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at <10.0 million years ago (MYA), rather than in situ diversification. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. The effects of Miocene paleogeographic events on Neotropical diversification dynamics provided the framework under which Quaternary patterns of endemism evolved. PMID:19278298

How does pollen versus seed dispersal affect niche evolution?

PubMed

Aguilée, Robin; Shaw, Frank H; Rousset, François; Shaw, Ruth G; Ronce, Ophélie

2013-03-01

In heterogeneous landscapes, the genetic and demographic consequences of dispersal influence the evolution of niche width. Unless pollen is limiting, pollen dispersal does not contribute directly to population growth. However, by disrupting local adaptation, it indirectly affects population dynamics. We compare the effect of pollen versus seed dispersal on the evolution of niche width in heterogeneous habitats, explicitly considering the feedback between maladaptation and demography. We consider two scenarios: the secondary contact of two subpopulations, in distinct, formerly isolated habitats, and the colonization of an empty habitat with dispersal between the new and ancestral habitat. With an analytical model, we identify critical levels of genetic variance leading to niche contraction (secondary contact scenario), or expansion (new habitat scenario). We confront these predictions with simulations where the genetic variance freely evolves. Niche contraction occurs when habitats are very different. It is faster as total gene flow increases or as pollen predominates in overall gene flow. Niche expansion occurs when habitat heterogeneity is not too high. Seed dispersal accelerates it, whereas pollen dispersal tends to retard it. In both scenarios very high seed dispersal leads to extinction. Overall, our results predict a wider niche for species dispersing seeds more than pollen. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Benchmarking novel approaches for modelling species range dynamics

PubMed Central

Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H.; Moore, Kara A.; Zimmermann, Niklaus E.

2016-01-01

Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species’ range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species’ response to climate change but also emphasise several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches operational for large numbers of species. PMID:26872305

Benchmarking novel approaches for modelling species range dynamics.

PubMed

Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

2016-08-01

Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches operational for large numbers of species. © 2016 John Wiley & Sons Ltd.

Late Quaternary climate change shapes island biodiversity.

PubMed

Weigelt, Patrick; Steinbauer, Manuel Jonas; Cabral, Juliano Sarmento; Kreft, Holger

2016-04-07

Island biogeographical models consider islands either as geologically static with biodiversity resulting from ecologically neutral immigration-extinction dynamics, or as geologically dynamic with biodiversity resulting from immigration-speciation-extinction dynamics influenced by changes in island characteristics over millions of years. Present climate and spatial arrangement of islands, however, are rather exceptional compared to most of the Late Quaternary, which is characterized by recurrent cooler and drier glacial periods. These climatic oscillations over short geological timescales strongly affected sea levels and caused massive changes in island area, isolation and connectivity, orders of magnitude faster than the geological processes of island formation, subsidence and erosion considered in island theory. Consequences of these oscillations for present biodiversity remain unassessed. Here we analyse the effects of present and Last Glacial Maximum (LGM) island area, isolation, elevation and climate on key components of angiosperm diversity on islands worldwide. We find that post-LGM changes in island characteristics, especially in area, have left a strong imprint on present diversity of endemic species. Specifically, the number and proportion of endemic species today is significantly higher on islands that were larger during the LGM. Native species richness, in turn, is mostly determined by present island characteristics. We conclude that an appreciation of Late Quaternary environmental change is essential to understand patterns of island endemism and its underlying evolutionary dynamics.

Long-term spatiotemporal stability and dynamic changes in helminth infracommunities of bank voles (Myodes glareolus) in NE Poland.

PubMed

Grzybek, Maciej; Bajer, Anna; Bednarska, Małgorzata; Al-Sarraf, Mohammed; Behnke-Borowczyk, Jolanta; Harris, Philip D; Price, Stephen J; Brown, Gabrielle S; Osborne, Sarah-Jane; Siński, Edward; Behnke, Jerzy M

2015-12-01

Parasites are considered to be an important selective force in host evolution but ecological studies of host-parasite systems are usually short-term providing only snap-shots of what may be dynamic systems. We have conducted four surveys of helminths of bank voles at three ecologically similar woodland sites in NE Poland, spaced over a period of 11 years, to assess the relative importance of temporal and spatial effects on helminth infracommunities. Some measures of infracommunity structure maintained relative stability: the rank order of prevalence and abundance of Heligmosomum mixtum, Heligmosomoides glareoli and Mastophorus muris changed little between the four surveys. Other measures changed markedly: dynamic changes were evident in Syphacia petrusewiczi which declined to local extinction, while the capillariid Aonchotheca annulosa first appeared in 2002 and then increased in prevalence and abundance over the remaining three surveys. Some species are therefore dynamic and both introductions and extinctions can be expected in ecological time. At higher taxonomic levels and for derived measures, year and host-age effects and their interactions with site are important. Our surveys emphasize that the site of capture is the major determinant of the species contributing to helminth community structure, providing some predictability in these systems.

Dynamic diffraction artefacts in Bragg coherent diffractive imaging

DOE PAGES

Hu, Wen; Huang, Xiaojing; Yan, Hanfei

2018-02-01

This article reports a theoretical study on the reconstruction artefacts in Bragg coherent diffractive imaging caused by dynamical diffraction effects. It is shown that, unlike the absorption and refraction effects that can be corrected after reconstruction, dynamical diffraction effects have profound impacts on both the amplitude and the phase of the reconstructed complex object, causing strong artefacts. At the dynamical diffraction limit, the reconstructed shape is no longer correct, as a result of the strong extinction effect. Simulations for hemispherical particles of different sizes show the type, magnitude and extent of the dynamical diffraction artefacts, as well as the conditionsmore » under which they are negligible.« less

On the intrinsic dynamics of bacteria in waterborne infections.

PubMed

Yang, Chayu; Wang, Jin

2018-02-01

The intrinsic dynamics of bacteria often play an important role in the transmission and spread of waterborne infectious diseases. In this paper, we construct mathematical models for waterborne infections and analyze two types of nontrivial bacterial dynamics: logistic growth, and growth with Allee effects. For the model with logistic growth, we find that regular threshold dynamics take place, and the basic reproduction number can be used to characterize disease extinction and persistence. In contrast, the model with Allee effects exhibits much more complex dynamics, including the existence of multiple endemic equilibria and the presence of backward bifurcation and forward hysteresis. Copyright © 2017 Elsevier Inc. All rights reserved.

Dynamic diffraction artefacts in Bragg coherent diffractive imaging.

PubMed

Hu, Wen; Huang, Xiaojing; Yan, Hanfei

2018-02-01

This article reports a theoretical study on the reconstruction artefacts in Bragg coherent diffractive imaging caused by dynamical diffraction effects. It is shown that, unlike the absorption and refraction effects that can be corrected after reconstruction, dynamical diffraction effects have profound impacts on both the amplitude and the phase of the reconstructed complex object, causing strong artefacts. At the dynamical diffraction limit, the reconstructed shape is no longer correct, as a result of the strong extinction effect. Simulations for hemispherical particles of different sizes show the type, magnitude and extent of the dynamical diffraction artefacts, as well as the conditions under which they are negligible.

Dynamic diffraction artefacts in Bragg coherent diffractive imaging

PubMed Central

Yan, Hanfei

2018-01-01

This article reports a theoretical study on the reconstruction artefacts in Bragg coherent diffractive imaging caused by dynamical diffraction effects. It is shown that, unlike the absorption and refraction effects that can be corrected after reconstruction, dynamical diffraction effects have profound impacts on both the amplitude and the phase of the reconstructed complex object, causing strong artefacts. At the dynamical diffraction limit, the reconstructed shape is no longer correct, as a result of the strong extinction effect. Simulations for hemispherical particles of different sizes show the type, magnitude and extent of the dynamical diffraction artefacts, as well as the conditions under which they are negligible. PMID:29507549

Badomics words and the power and peril of the ome-meme

PubMed Central

2012-01-01

Languages and cultures, like organisms, are constantly evolving. Words, like genes, can come and go–spreading around or going extinct. Here I discuss the spread of one small subset of words that are meant to convey “comprehensiveness” in some way: the “omes” and other words derived from “genome” or “genomics.” I focus on a bad aspect of this spread the use of what I refer to as “badomics” words. I discuss why these should be considered bad and how to distinguish badomics words from good ones. PMID:23587201

Insect diversity in the fossil record

NASA Technical Reports Server (NTRS)

Labandeira, C. C.; Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

1993-01-01

Insects possess a surprisingly extensive fossil record. Compilation of the geochronologic ranges of insect families demonstrates that their diversity exceeds that of preserved vertebrate tetrapods through 91 percent of their evolutionary history. The great diversity of insects was achieved not by high origination rates but rather by low extinction rates comparable to the low rates of slowly evolving marine invertebrate groups. The great radiation of modern insects began 245 million years ago and was not accelerated by the expansion of angiosperms during the Cretaceous period. The basic trophic machinery of insects was in place nearly 100 million years before angiosperms appeared in the fossil record.

Late Quaternary Megafaunal Extinctions in Northern Eurasia: Latest Results

NASA Astrophysics Data System (ADS)

Stuart, Anthony

2010-05-01

Anthony J. Stuart1 & Adrian M. Lister2 1 Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK. Email: tony.s@megafauna.org.uk 2 Department of Palaeontology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK. Email: a.lister@nhm.ac.uk. The global extinction of many spectacular species of megafauna (large terrestrial mammals, together with a few large reptiles and birds) within the last c. 50,000 years (Late Quaternary) has been attributed on the one hand to ‘overkill' by human hunters and on the other to environmental change. However, in spite of more than half a century of active interest and research the issue remains unresolved, largely because there are insufficient dated records of megafaunal species for most parts of the world. Northern Eurasia is an especially fruitful region in which to research megafaunal extinctions as it has a wealth of megafaunal material and crucially most extinctions occurred well within the range of radiocarbon dating. Our approach, in a series of projects over the last decade funded by the UK Natural Environment Research Council (NERC), involves amassing radiocarbon dates made directly on megafaunal material from across the entire region: a) by submitting a substantial number of samples (so far c. 500 dates) for AMS dating at Oxford (ORAU); b) obtaining AMS dates from colleagues working on aDNA projects; and c) carefully screening (‘auditing') dates from the literature. The dates (calibrated using OxCal) are plotted as time-sliced maps and as chronological/geographical charts. In our previous work we targeted a range of extinct species from Northern Eurasia: woolly mammoth, woolly rhinoceros, giant deer, cave bear (in collaboration with Martina Pacher), cave lion, and spotted hyaena (which survives today only in Sub-Saharan Africa). By this means we have established a reliable chronology for these extinctions which we are able to compare with the climatic, vegetational and archaeological records in collaboration with colleagues at Durham University, Royal Holloway, University of London and Southampton University. It is clear from the results that environmental change had a major impact, but the geographical and chronological patterns are complex and there is striking variation in extinction dynamics between species. For example cave bear and spotted hyaena show early extinction in Europe c.28 cal ka, whereas cave lion and woolly rhino disappeared in the Late Glacial c.14 cal ka, and mammoth and giant deer persisted in limited areas well into the Holocene. Our current NERC funded project (3 years from March 2009) extends the scope of our research to include several species that survive to the present day: e.g. musk ox, reindeer, horse, red deer, and moose, and is also extended geographically to Alaska, and the Yukon. Modelling of vegetational changes during the last 40,000 years (by our colleagues at Durham: Judy Allen, Yvonne Collingham, Brian Huntley, using LPJ-Guess data from Paul Valdes) is providing much better geographical coverage than the available pollen data, and also structure and productivity of the vegetation - both of considerable importance to the mammal fauna. Comparing the chronological and geographical dynamics of extant and extinct species promises to shed light on why some species were lost whereas others survived. Moreover, by using a niche-modelling approach we hope to show whether or not species became extinct due to habitat loss, or whether other factors such as human hunting might have been involved in their final disappearance.

The Molecular Motor KIF21B Mediates Synaptic Plasticity and Fear Extinction by Terminating Rac1 Activation.

PubMed

Morikawa, Momo; Tanaka, Yosuke; Cho, Hyun-Soo; Yoshihara, Masaharu; Hirokawa, Nobutaka

2018-06-26

Fear extinction is a component of cognitive flexibility that is relevant for important psychiatric diseases, but its molecular mechanism is still largely elusive. We established mice lacking the kinesin-4 motor KIF21B as a model for fear extinction defects. Postsynaptic NMDAR-dependent long-term depression (LTD) is specifically impaired in knockouts. NMDAR-mediated LTD-causing stimuli induce dynamic association of KIF21B with the Rac1GEF subunit engulfment and cell motility protein 1 (ELMO1), leading to ELMO1 translocation out of dendritic spines and its sequestration in endosomes. This process may essentially terminate transient activation of Rac1, shrink spines, facilitate AMPAR endocytosis, and reduce postsynaptic strength, thereby forming a mechanistic link to LTD expression. Antagonizing ELMO1/Dock Rac1GEF activity by the administration of 4-[3'-(2″-chlorophenyl)-2'-propen-1'-ylidene]-1-phenyl-3,5-pyrazolidinedione (CPYPP) significantly reverses the knockout phenotype. Therefore, we propose that KIF21B-mediated Rac1 inactivation is a key molecular event in NMDAR-dependent LTD expression underlying cognitive flexibility in fear extinction. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Population extinction under bursty reproduction in a time-modulated environment

NASA Astrophysics Data System (ADS)

Vilk, Ohad; Assaf, Michael

2018-06-01

In recent years nondemographic variability has been shown to greatly affect dynamics of stochastic populations. For example, nondemographic noise in the form of a bursty reproduction process with an a priori unknown burst size, or environmental variability in the form of time-varying reaction rates, have been separately found to dramatically impact the extinction risk of isolated populations. In this work we investigate the extinction risk of an isolated population under the combined influence of these two types of nondemographic variation. Using the so-called momentum-space Wentzel-Kramers-Brillouin (WKB) approach and accounting for the explicit time dependence in the reaction rates, we arrive at a set of time-dependent Hamilton equations. To this end, we evaluate the population's extinction risk by finding the instanton of the time-perturbed Hamiltonian numerically, whereas analytical expressions are presented in particular limits using various perturbation techniques. We focus on two classes of time-varying environments: periodically varying rates corresponding to seasonal effects and a sudden decrease in the birth rate corresponding to a catastrophe. All our theoretical results are tested against numerical Monte Carlo simulations with time-dependent rates and also against a numerical solution of the corresponding time-dependent Hamilton equations.

Life and extinction of megafauna in the ice-age Arctic

PubMed Central

Mann, Daniel H.; Groves, Pamela; Reanier, Richard E.; Gaglioti, Benjamin V.; Kunz, Michael L.; Shapiro, Beth

2015-01-01

Understanding the population dynamics of megafauna that inhabited the mammoth steppe provides insights into the causes of extinctions during both the terminal Pleistocene and today. Our study area is Alaska's North Slope, a place where humans were rare when these extinctions occurred. After developing a statistical approach to remove the age artifacts caused by radiocarbon calibration from a large series of dated megafaunal bones, we compare the temporal patterns of bone abundance with climate records. Megafaunal abundance tracked ice age climate, peaking during transitions from cold to warm periods. These results suggest that a defining characteristic of the mammoth steppe was its temporal instability and imply that regional extinctions followed by population reestablishment from distant refugia were characteristic features of ice-age biogeography at high latitudes. It follows that long-distance dispersal was crucial for the long-term persistence of megafaunal species living in the Arctic. Such dispersal was only possible when their rapidly shifting range lands were geographically interconnected. The end of the last ice age was fatally unique because the geographic ranges of arctic megafauna became permanently fragmented after stable, interglacial climate engendered the spread of peatlands at the same time that rising sea level severed former dispersal routes. PMID:26578776

Ancient phylogenetic divergence of the enigmatic African rodent Zenkerella and the origin of anomalurid gliding

PubMed Central

Fernández, David; Sallam, Hesham M.; Cronin, Drew T.; Esara Echube, José Manuel

2016-01-01

The “scaly-tailed squirrels” of the rodent family Anomaluridae have a long evolutionary history in Africa, and are now represented by two gliding genera (Anomalurus and Idiurus) and a rare and obscure genus (Zenkerella) that has never been observed alive by mammalogists. Zenkerella shows no anatomical adaptations for gliding, but has traditionally been grouped with the glider Idiurus on the basis of craniodental similarities, implying that either the Zenkerella lineage lost its gliding adaptations, or that Anomalurus and Idiurus evolved theirs independently. Here we present the first nuclear and mitochondrial DNA sequences of Zenkerella, based on recently recovered whole-body specimens from Bioko Island (Equatorial Guinea), which show unambiguously that Zenkerella is the sister taxon of Anomalurus and Idiurus. These data indicate that gliding likely evolved only once within Anomaluridae, and that there were no subsequent evolutionary reversals. We combine this new molecular evidence with morphological data from living and extinct anomaluromorph rodents and estimate that the lineage leading to Zenkerella has been evolving independently in Africa since the early Eocene, approximately 49 million years ago. Recently discovered fossils further attest to the antiquity of the lineage leading to Zenkerella, which can now be recognized as a classic example of a “living fossil,” about which we know remarkably little. The osteological markers of gliding are estimated to have evolved along the stem lineage of the Anomalurus–Idiurus clade by the early Oligocene, potentially indicating that this adaptation evolved in response to climatic perturbations at the Eocene–Oligocene boundary (∼34 million years ago). PMID:27602286

Population dynamical behavior of Lotka-Volterra system under regime switching

NASA Astrophysics Data System (ADS)

Li, Xiaoyue; Jiang, Daqing; Mao, Xuerong

2009-10-01

In this paper, we investigate a Lotka-Volterra system under regime switching where B(t) is a standard Brownian motion. The aim here is to find out what happens under regime switching. We first obtain the sufficient conditions for the existence of global positive solutions, stochastic permanence and extinction. We find out that both stochastic permanence and extinction have close relationships with the stationary probability distribution of the Markov chain. The limit of the average in time of the sample path of the solution is then estimated by two constants related to the stationary distribution and the coefficients. Finally, the main results are illustrated by several examples.

Transitions or turnovers? Climatically-forced extinctions of Homo sapiens and Neanderthals in the east Mediterranean Levant

NASA Astrophysics Data System (ADS)

Shea, John J.

2008-11-01

The East Mediterranean Levant is a focal point for debate about evolutionary continuity among Late Pleistocene hominin populations. Changes in the Levantine Middle and Upper Palaeolithic archaeological records are almost invariably described in terms of adaptive shifts and behavioural transitions, rather than as changes in hominin populations. This paper examines evidence for hominin evolutionary continuity in the Levant between 130 and 25 ka. Two inflection points, one within the Middle Palaeolithic ca 75 ka and the other between the Middle and Upper Palaeolithic ca 45 ka, are examined in light of recently-discovered evidence for rapid climate change and environmental deterioration. It is proposed that both periods mark regional extinctions and turnovers of hominin populations. The first of these occurred among early Homo sapiens, the second among Neanderthals. Each event was followed by dispersal of hominin populations into the Levant from adjacent regions. Differences in Middle vs. Upper Palaeolithic Homo sapiens' long-term success in the Levant may reflect recently-evolved strategies for coping with rapid climate change and with colder arid habitats.

Taxonomic revision and phylogenetic analysis of the flightless Mancallinae (Aves, Pan-Alcidae)

PubMed Central

Smith, Neil Adam

2011-01-01

Abstract Although flightless alcids from the Miocene and Pliocene of the eastern Pacific Ocean have been known for over 100 years, there is no detailed evaluation of diversity and systematic placement of these taxa. This is the first combined analysis of morphological and molecular data to include all extant alcids, the recently extinct Great Auk Pinguinus impennis, the mancalline auks, and a large outgroup sampling of 29 additional non-alcid charadriiforms. Based on the systematic placement of Mancallinae outside of crown clade Alcidae, the clade name Pan-Alcidae is proposed to include all known alcids. An extensive review of the Mancallinae fossil record resulted in taxonomic revision of the clade, and identification of three new species. In addition to positing the first hypothesis of inter-relationships between Mancallinae species, phylogenetic results support placement of Mancallinae as the sister taxon to all other Alcidae, indicating that flightlessness evolved at least twice in the alcid lineage. Convergent osteological characteristics of Mancallinae, the flightless Great Auk, and Spheniscidae are summarized, and implications of Mancallinae diversity, radiation, and extinction in the context of paleoclimatic changes are discussed. PMID:21594108

A new model for extinction and recolonization in two dimensions: quantifying phylogeography.

PubMed

Barton, Nicholas H; Kelleher, Jerome; Etheridge, Alison M

2010-09-01

Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci. © 2010 The Author(s). Journal compilation © 2010 The Society for the Study of Evolution.

Cephalopod embryonic shells as a tool to reconstruct reproductive strategies in extinct taxa.

PubMed

Laptikhovsky, Vladimir; Nikolaeva, Svetlana; Rogov, Mikhail

2018-02-01

An exhaustive study of existing data on the relationship between egg size and maximum size of embryonic shells in 42 species of extant cephalopods demonstrated that these values are approximately equal regardless of taxonomy and shell morphology. Egg size is also approximately equal to mantle length of hatchlings in 45 cephalopod species with rudimentary shells. Paired data on the size of the initial chamber versus embryonic shell in 235 species of Ammonoidea, 46 Bactritida, 13 Nautilida, 22 Orthocerida, 8 Tarphycerida, 4 Oncocerida, 1 Belemnoidea, 4 Sepiida and 1 Spirulida demonstrated that, although there is a positive relationship between these parameters in some taxa, initial chamber size cannot be used to predict egg size in extinct cephalopods; the size of the embryonic shell may be more appropriate for this task. The evolution of reproductive strategies in cephalopods in the geological past was marked by an increasing significance of small-egged taxa, as is also seen in simultaneously evolving fish taxa. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Inference of Time-Evolving Coupled Dynamical Systems in the Presence of Noise

NASA Astrophysics Data System (ADS)

Stankovski, Tomislav; Duggento, Andrea; McClintock, Peter V. E.; Stefanovska, Aneta

2012-07-01

A new method is introduced for analysis of interactions between time-dependent coupled oscillators, based on the signals they generate. It distinguishes unsynchronized dynamics from noise-induced phase slips and enables the evolution of the coupling functions and other parameters to be followed. It is based on phase dynamics, with Bayesian inference of the time-evolving parameters achieved by shaping the prior densities to incorporate knowledge of previous samples. The method is tested numerically and applied to reveal and quantify the time-varying nature of cardiorespiratory interactions.

Discrete two-sex models of population dynamics: On modelling the mating function

NASA Astrophysics Data System (ADS)

Bessa-Gomes, Carmen; Legendre, Stéphane; Clobert, Jean

2010-09-01

Although sexual reproduction has long been a central subject of theoretical ecology, until recently its consequences for population dynamics were largely overlooked. This is now changing, and many studies have addressed this issue, showing that when the mating system is taken into account, the population dynamics depends on the relative abundance of males and females, and is non-linear. Moreover, sexual reproduction increases the extinction risk, namely due to the Allee effect. Nevertheless, different studies have identified diverse potential consequences, depending on the choice of mating function. In this study, we investigate the consequences of three alternative mating functions that are frequently used in discrete population models: the minimum; the harmonic mean; and the modified harmonic mean. We consider their consequences at three levels: on the probability that females will breed; on the presence and intensity of the Allee effect; and on the extinction risk. When we consider the harmonic mean, the number of times the individuals of the least abundant sex mate exceeds their mating potential, which implies that with variable sex-ratios the potential reproductive rate is no longer under the modeller's control. Consequently, the female breeding probability exceeds 1 whenever the sex-ratio is male-biased, which constitutes an obvious problem. The use of the harmonic mean is thus only justified if we think that this parameter should be re-defined in order to represent the females' breeding rate and the fact that females may reproduce more than once per breeding season. This phenomenon buffers the Allee effect, and reduces the extinction risk. However, when we consider birth-pulse populations, such a phenomenon is implausible because the number of times females can reproduce per birth season is limited. In general, the minimum or modified harmonic mean mating functions seem to be more suitable for assessing the impact of mating systems on population dynamics.

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation.

PubMed

Pigot, Alex L; Phillimore, Albert B; Owens, Ian P F; Orme, C David L

2010-12-01

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.

Dynamic Weakening (Extinction) of Simple Hydrocarbon-air Counterflow Diffusion Flames by Oscillatory Inflows

NASA Technical Reports Server (NTRS)

Pellett, G.; Kabaria, A.; Panigrahi, B.; Sammons, K.; Convery, J.; Wilson, L.

2005-01-01

This study of laminar non-premixed HC-air flames used an Oscillatory-input Opposed Jet Burner (OOJB) system developed from a previously well-characterized 7.2-mm Pyrex-nozzle OJB system. Over 600 dynamic Flame Strength (FS) measurements were obtained on unanchored (free-floating) laminar Counterflow Diffusion Flames (CFDF's). Flames were stabilized using plug inflows having steady-plus-sinusoidal axial velocities of varied magnitude, frequency, f, up to 1600 Hz, and phase angle from 0 (most data) to 360 degrees. Dynamic FS is defined as the maximum average air input velocity (U(sub air), at nozzle exit) a CFDF can sustain before strain-induced extinction occurs due to prescribed oscillatory peak-to-peak velocity inputs superimposed on steady inputs. Initially, dynamic flame extinction data were obtained at low f, and were supported by 25-120 Hz Hot-Wire cold-flow velocity data at nozzle exits. Later, expanded extinction data were supported by 4-1600 Hz Probe Microphone (PM) pk/pk P data at nozzle exits. The PM data were first obtained without flows, and later with cold stagnating flows, which better represent speaker-diaphragm dynamics during runs. The PM approach enabled characterizations of Dynamic Flame Weakening (DFW) of CFDF's from 8 to 1600 Hz. DFW was defined as % decrease in FS per Pascal of pk/pk P oscillation, namely, DFW = - 100 d(U(sub air) / U(sub air),0Hz) / d(pkpk P). The linear normalization with respect to acoustic pressure magnitude (and steady state (SS) FS) led to a DFW unaffected by strong internal resonances. For the C2H4/N2-air system, from 8 to 20 Hz, DFW is constant at 8.52 plus or minus 0.20 (% weakening)/Pa. This reflects a quasi-steady flame response to an acoustically induced dU(sub air)/dP. Also, it is surprisingly independent of C2H4/N2 mole fraction due to normalization by SS FS. From 20 to approximately 150 Hz, the C2H4/N2 air-flames weakened progressively less, with an inflection at approximately 70 Hz, and became asymptotically insensitive (DFW approximately 0) at approximately 300 Hz, which continued to 1600 Hz. The DFW of CH4-air flames followed a similar pattern, but showed much greater weakening than C2H4/N2-air flames; i.e., the quasi-steady DFW (8 to approximately 15 Hz) was 44.3 %/Pa, or approximately 5x larger, even though the 0 Hz (SS) FS was only 3.0 x smaller. The quasi-steady DFW's of C3H8-air and C2H6-air were intermediate at 34.8 and 20.9 %Pa, respectively. The DFW profiles of all four fuels, at various frequencies, correlated well but non-linearly with respective SS FS's. Notably, the DFW profile for C3H8 air fell more rapidly in the range greater than 15 to 60 Hz, compared with the 1- and 2-carbon fuels. This may indicate a shift in chemical kinetics, and/or O2 transport to a flame that moved closer to the fuel-side. In conclusion, Dynamic Flame Weakening limits appear significant and unique for each fuel, and correlate closely, but non-linearly, with Steady-State Flame Strengths at any given frequency. For reasons unknown, the dynamic flames didn't weaken more at intermediate frequencies (e.g., at 20-50 Hz) than they did at low frequencies (less than 15 Hz), where quasi-steady weakening appears to dominate. Quasi-steady flame weakening ostensibly represents a transient input strain rate maximum that just exceeds the steady-state strain-rate-limited extinction limit for a few cycles. Clearly, further detailed mechanistic understanding is needed in the fall-off region.

Parks or Prisons?

ERIC Educational Resources Information Center

Thomson, Gareth

1998-01-01

Presents a simulation activity in which students assume the role of grizzly bears in Banff National Park. Concepts such as species diversity, fitness, natural selection, habitat loss, extinction, and population dynamics are discussed. Children learn how human activities can affect the bear's reproductive success. Lists materials, instructional…

Host persistence or extinction from emerging infectious disease: insights from white-nose syndrome in endemic and invading regions.

PubMed

Hoyt, Joseph R; Langwig, Kate E; Sun, Keping; Lu, Guanjun; Parise, Katy L; Jiang, Tinglei; Frick, Winifred F; Foster, Jeffrey T; Feng, Jiang; Kilpatrick, A Marm

2016-03-16

Predicting species' fates following the introduction of a novel pathogen is a significant and growing problem in conservation. Comparing disease dynamics between introduced and endemic regions can offer insight into which naive hosts will persist or go extinct, with disease acting as a filter on host communities. We examined four hypothesized mechanisms for host-pathogen persistence by comparing host infection patterns and environmental reservoirs for Pseudogymnoascus destructans (the causative agent of white-nose syndrome) in Asia, an endemic region, and North America, where the pathogen has recently invaded. Although colony sizes of bats and hibernacula temperatures were very similar, both infection prevalence and fungal loads were much lower on bats and in the environment in Asia than North America. These results indicate that transmission intensity and pathogen growth are lower in Asia, likely due to higher host resistance to pathogen growth in this endemic region, and not due to host tolerance, lower transmission due to smaller populations, or lower environmentally driven pathogen growth rate. Disease filtering also appears to be favouring initially resistant species in North America. More broadly, determining the mechanisms allowing species persistence in endemic regions can help identify species at greater risk of extinction in introduced regions, and determine the consequences for disease dynamics and host-pathogen coevolution. © 2016 The Author(s).

Interstellar Object ’Oumuamua as an Extinct Fragment of an Ejected Cometary Planetesimal

NASA Astrophysics Data System (ADS)

Raymond, Sean N.; Armitage, Philip J.; Veras, Dimitri

2018-03-01

’Oumuamua was discovered passing through our solar system on a hyperbolic orbit. It presents an apparent contradiction, with colors similar to those of volatile-rich solar system bodies but with no visible outgassing or activity during its close approach to the Sun. Here, we show that this contradiction can be explained by the dynamics of planetesimal ejection by giant planets. We propose that ’Oumuamua is an extinct fragment of a comet-like planetesimal born a planet-forming disk that also formed Neptune- to Jupiter-mass giant planets. On its pathway to ejection ’Oumuamua’s parent body underwent a close encounter with a giant planet and was tidally disrupted into small pieces, similar to comet Shoemaker–Levy 9’s disruption after passing close to Jupiter. We use dynamical simulations to show that 0.1%–1% of cometary planetesimals undergo disruptive encounters prior to ejection. Rocky asteroidal planetesimals are unlikely to disrupt due to their higher densities. After disruption, the bulk of fragments undergo enough close passages to their host stars to lose their surface volatiles and become extinct. Planetesimal fragments such as ’Oumuamua contain little of the mass in the population of interstellar objects but dominate by number. Our model makes predictions that will be tested in the coming decade by the Large Synoptic Survey Telescope.

Detecting intrinsic dynamics of traffic flow with recurrence analysis and empirical mode decomposition

NASA Astrophysics Data System (ADS)

Xiong, Hui; Shang, Pengjian; Bian, Songhan

2017-05-01

In this paper, we apply the empirical mode decomposition (EMD) method to the recurrence plot (RP) and recurrence quantification analysis (RQA), to evaluate the frequency- and time-evolving dynamics of the traffic flow. Based on the cumulative intrinsic mode functions extracted by the EMD, the frequency-evolving RP regarding different oscillation of modes suggests that apparent dynamics of the data considered are mainly dominated by its components of medium- and low-frequencies while severely affected by fast oscillated noises contained in the signal. Noises are then eliminated to analyze the intrinsic dynamics and consequently, the denoised time-evolving RQA diversely characterizes the properties of the signal and marks crucial points more accurately where white bands in the RP occur, whereas a strongly qualitative agreement exists between all the non-denoised RQA measures. Generally, the EMD combining with the recurrence analysis sheds more reliable, abundant and inherent lights into the traffic flow, which is meaningful to the empirical analysis of complex systems.

The Evolution of Diapsid Reproductive Strategy with Inferences about Extinct Taxa.

PubMed

Moore, Jason R; Varricchio, David J

2016-01-01

Diapsids show an extremely wide range of reproductive strategies. Offspring may receive no parental care, care from only one sex, care from both parents, or care under more complex regimes. Young may vary from independent, super-precocial hatchlings to altricial neonates needing much care before leaving the nest. Parents can invest heavily in a few young, or less so in a larger number. Here we examine the evolution of these traits across a composite phylogeny spanning the extant diapsids and including the limited number of extinct taxa for which reproductive strategies can be well constrained. Generalized estimating equation(GEE)-based phylogenetic comparative methods demonstrate the influences of body mass, parental care strategy and hatchling maturity on clutch volume across the diapsids. The influence of polygamous reproduction is not important despite a large sample size. Applying the results of these models to the dinosaurs supports the hypothesis of paternal care (male only) in derived non-avian theropods, previously suggested based on simpler analyses. These data also suggest that sauropodomorphs did not care for their young. The evolution of parental-care occurs in an almost linear series of transitions. Paternal care rarely gives rise to other care strategies. Where hatchling condition changes, diapsids show an almost unidirectional tendency of evolution towards increased altriciality. Transitions to social monogamy from the ancestral state in diapsids, where both sexes are polygamous, are common. In contrast, once evolved, polygyny and polyandry are very evolutionarily stable. Polygyny and maternal care correlate, as do polyandry and paternal care. Ancestral-character estimation (ACE) of these care strategies with the character transition likelihoods estimated from the original data gives good confidence at most important nodes. These analyses suggest that the basalmost diapsids had no parental care. Crocodilians independently evolved maternal care, paternal care evolved in the saurischian line, prior to derived theropod dinosaurs, and the most basal neognaths likely exhibited biparental care. Overall, the evolution of parental care among diapsids shows a persistent trend towards increased care of offspring, and more complex care strategies and behaviors with time. Reversions to reduced care are infrequent.

Biomechanics of running indicates endothermy in bipedal dinosaurs.

PubMed

Pontzer, Herman; Allen, Vivian; Hutchinson, John R

2009-11-11

One of the great unresolved controversies in paleobiology is whether extinct dinosaurs were endothermic, ectothermic, or some combination thereof, and when endothermy first evolved in the lineage leading to birds. Although it is well established that high, sustained growth rates and, presumably, high activity levels are ancestral for dinosaurs and pterosaurs (clade Ornithodira), other independent lines of evidence for high metabolic rates, locomotor costs, or endothermy are needed. For example, some studies have suggested that, because large dinosaurs may have been homeothermic due to their size alone and could have had heat loss problems, ectothermy would be a more plausible metabolic strategy for such animals. Here we describe two new biomechanical approaches for reconstructing the metabolic rate of 14 extinct bipedal dinosauriforms during walking and running. These methods, well validated for extant animals, indicate that during walking and slow running the metabolic rate of at least the larger extinct dinosaurs exceeded the maximum aerobic capabilities of modern ectotherms, falling instead within the range of modern birds and mammals. Estimated metabolic rates for smaller dinosaurs are more ambiguous, but generally approach or exceed the ectotherm boundary. Our results support the hypothesis that endothermy was widespread in at least larger non-avian dinosaurs. It was plausibly ancestral for all dinosauriforms (perhaps Ornithodira), but this is perhaps more strongly indicated by high growth rates than by locomotor costs. The polarity of the evolution of endothermy indicates that rapid growth, insulation, erect postures, and perhaps aerobic power predated advanced "avian" lung structure and high locomotor costs.

A Triassic plesiosaurian skeleton and bone histology inform on evolution of a unique body plan

PubMed Central

Wintrich, Tanja; Hayashi, Shoji; Houssaye, Alexandra; Nakajima, Yasuhisa; Sander, P. Martin

2017-01-01

Secondary marine adaptation is a major pattern in amniote evolution, accompanied by specific bone histological adaptations. In the aftermath of the end-Permian extinction, diverse marine reptiles evolved early in the Triassic. Plesiosauria is the most diverse and one of the longest-lived clades of marine reptiles, but its bone histology is least known among the major marine amniote clades. Plesiosaurians had a unique and puzzling body plan, sporting four evenly shaped pointed flippers and (in most clades) a small head on a long, stiffened neck. The flippers were used as hydrofoils in underwater flight. A wide temporal, morphological, and morphometric gap separates plesiosaurians from their closest relatives (basal pistosaurs, Bobosaurus). For nearly two centuries, plesiosaurians were thought to appear suddenly in the earliest Jurassic after the end-Triassic extinctions. We describe the first Triassic plesiosaurian, from the Rhaetian of Germany, and compare its long bone histology to that of later plesiosaurians sampled for this study. The new taxon is recovered as a basal member of the Pliosauridae, revealing that diversification of plesiosaurians was a Triassic event and that several lineages must have crossed into the Jurassic. Plesiosaurian histology is strikingly uniform and different from stem sauropterygians. Histology suggests the concurrent evolution of fast growth and an elevated metabolic rate as an adaptation to cruising and efficient foraging in the open sea. The new specimen corroborates the hypothesis that open ocean life of plesiosaurians facilitated their survival of the end-Triassic extinctions. PMID:29242826

Virtual Genomes in Flux: An Interplay of Neutrality and Adaptability Explains Genome Expansion and Streamlining

PubMed Central

Cuypers, Thomas D.; Hogeweg, Paulien

2012-01-01

The picture that emerges from phylogenetic gene content reconstructions is that genomes evolve in a dynamic pattern of rapid expansion and gradual streamlining. Ancestral organisms have been estimated to possess remarkably rich gene complements, although gene loss is a driving force in subsequent lineage adaptation and diversification. Here, we study genome dynamics in a model of virtual cells evolving to maintain homeostasis. We observe a pattern of an initial rapid expansion of the genome and a prolonged phase of mutational load reduction. Generally, load reduction is achieved by the deletion of redundant genes, generating a streamlining pattern. Load reduction can also occur as a result of the generation of highly neutral genomic regions. These regions can expand and contract in a neutral fashion. Our study suggests that genome expansion and streamlining are generic patterns of evolving systems. We propose that the complex genotype to phenotype mapping in virtual cells as well as in their biological counterparts drives genome size dynamics, due to an emerging interplay between adaptation, neutrality, and evolvability. PMID:22234601

Modeling Temporal Behavior in Large Networks: A Dynamic Mixed-Membership Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossi, R; Gallagher, B; Neville, J

Given a large time-evolving network, how can we model and characterize the temporal behaviors of individual nodes (and network states)? How can we model the behavioral transition patterns of nodes? We propose a temporal behavior model that captures the 'roles' of nodes in the graph and how they evolve over time. The proposed dynamic behavioral mixed-membership model (DBMM) is scalable, fully automatic (no user-defined parameters), non-parametric/data-driven (no specific functional form or parameterization), interpretable (identifies explainable patterns), and flexible (applicable to dynamic and streaming networks). Moreover, the interpretable behavioral roles are generalizable, computationally efficient, and natively supports attributes. We applied ourmore » model for (a) identifying patterns and trends of nodes and network states based on the temporal behavior, (b) predicting future structural changes, and (c) detecting unusual temporal behavior transitions. We use eight large real-world datasets from different time-evolving settings (dynamic and streaming). In particular, we model the evolving mixed-memberships and the corresponding behavioral transitions of Twitter, Facebook, IP-Traces, Email (University), Internet AS, Enron, Reality, and IMDB. The experiments demonstrate the scalability, flexibility, and effectiveness of our model for identifying interesting patterns, detecting unusual structural transitions, and predicting the future structural changes of the network and individual nodes.« less

Bubble and Drop Nonlinear Dynamics (BDND)

NASA Technical Reports Server (NTRS)

Trinh, E. H.; Leal, L. Gary; Thomas, D. A.; Crouch, R. K.

1998-01-01

Free drops and bubbles are weakly nonlinear mechanical systems that are relatively simple to characterize experimentally in 1-G as well as in microgravity. The understanding of the details of their motion contributes to the fundamental study of nonlinear phenomena and to the measurement of the thermophysical properties of freely levitated melts. The goal of this Glovebox-based experimental investigation is the low-gravity assessment of the capabilities of a modular apparatus based on ultrasonic resonators and on the pseudo- extinction optical method. The required experimental task is the accurate measurements of the large-amplitude dynamics of free drops and bubbles in the absence of large biasing influences such as gravity and levitation fields. A single-axis levitator used for the positioning of drops in air, and an ultrasonic water-filled resonator for the trapping of air bubbles have been evaluated in low-gravity and in 1-G. The basic feasibility of drop positioning and shape oscillations measurements has been verified by using a laptop-interfaced automated data acquisition and the optical extinction technique. The major purpose of the investigation was to identify the salient technical issues associated with the development of a full-scale Microgravity experiment on single drop and bubble dynamics.

The impact of 850,000 years of climate changes on the structure and dynamics of mammal food webs.

PubMed

Nenzén, Hedvig K; Montoya, Daniel; Varela, Sara

2014-01-01

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities.

The Impact of 850,000 Years of Climate Changes on the Structure and Dynamics of Mammal Food Webs

PubMed Central

Nenzén, Hedvig K.; Montoya, Daniel; Varela, Sara

2014-01-01

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities. PMID:25207754

Medial prefrontal pathways for the contextual regulation of extinguished fear in humans

PubMed Central

Åhs, Fredrik; Kragel, Philip A.; Zielinski, David J.; Brady, Rachael; LaBar, Kevin S.

2015-01-01

The maintenance of anxiety disorders is thought to depend, in part, on deficits in extinction memory, possibly due to reduced contextual control of extinction that leads to fear renewal. Animal studies suggest that the neural circuitry responsible fear renewal includes the hippocampus, amygdala, and dorsomedial (dmPFC) and ventromedial (vmPFC) prefrontal cortex. However, the neural mechanisms of context-dependent fear renewal in humans remain poorly understood. We used functional magnetic resonance imaging (fMRI), combined with psychophysiology and immersive virtual reality, to elucidate how the hippocampus, amygdala, and dmPFC and vmPFC interact to drive the context-dependent renewal of extinguished fear. Healthy human participants encountered dynamic fear-relevant conditioned stimuli (CSs) while navigating through 3-D virtual reality environments in the MRI scanner. Conditioning and extinction were performed in two different virtual contexts. Twenty-four hours later, participants were exposed to the CSs without reinforcement while navigating through both contexts in the MRI scanner. Participants showed enhanced skin conductance responses (SCRs) to the previously-reinforced CS+ in the acquisition context on Day 2, consistent with fear renewal, and sustained responses in the dmPFC. In contrast, participants showed low SCRs to the CSs in the extinction context on Day 2, consistent with extinction recall, and enhanced vmPFC activation to the non-reinforced CS−. Structural equation modeling revealed that the dmPFC fully mediated the effect of the hippocampus on right amygdala activity during fear renewal, whereas the vmPFC partially mediated the effect of the hippocampus on right amygdala activity during extinction recall. These results indicate dissociable contextual influences of the hippocampus on prefrontal pathways, which, in turn, determine the level of reactivation of fear associations. PMID:26220745

Drastic population fluctuations explain the rapid extinction of the passenger pigeon.

PubMed

Hung, Chih-Ming; Shaner, Pei-Jen L; Zink, Robert M; Liu, Wei-Chung; Chu, Te-Chin; Huang, Wen-San; Li, Shou-Hsien

2014-07-22

To assess the role of human disturbances in species' extinction requires an understanding of the species population history before human impact. The passenger pigeon was once the most abundant bird in the world, with a population size estimated at 3-5 billion in the 1800s; its abrupt extinction in 1914 raises the question of how such an abundant bird could have been driven to extinction in mere decades. Although human exploitation is often blamed, the role of natural population dynamics in the passenger pigeon's extinction remains unexplored. Applying high-throughput sequencing technologies to obtain sequences from most of the genome, we calculated that the passenger pigeon's effective population size throughout the last million years was persistently about 1/10,000 of the 1800's estimated number of individuals, a ratio 1,000-times lower than typically found. This result suggests that the passenger pigeon was not always super abundant but experienced dramatic population fluctuations, resembling those of an "outbreak" species. Ecological niche models supported inference of drastic changes in the extent of its breeding range over the last glacial-interglacial cycle. An estimate of acorn-based carrying capacity during the past 21,000 y showed great year-to-year variations. Based on our results, we hypothesize that ecological conditions that dramatically reduced population size under natural conditions could have interacted with human exploitation in causing the passenger pigeon's rapid demise. Our study illustrates that even species as abundant as the passenger pigeon can be vulnerable to human threats if they are subject to dramatic population fluctuations, and provides a new perspective on the greatest human-caused extinction in recorded history.

The path to host extinction can lead to loss of generalist parasites.

PubMed

Farrell, Maxwell J; Stephens, Patrick R; Berrang-Ford, Lea; Gittleman, John L; Davies, T Jonathan

2015-07-01

Host extinction can alter disease transmission dynamics, influence parasite extinction and ultimately change the nature of host-parasite systems. While theory predicts that single-host parasites are among the parasite species most susceptible to extinction following declines in their hosts, documented parasite extinctions are rare. Using a comparative approach, we investigate how the richness of single-host and multi-host parasites is influenced by extinction risk among ungulate and carnivore hosts. Host-parasite associations for free-living carnivores (order Carnivora) and terrestrial ungulates (orders Perissodactyla + Cetartiodactyla minus cetaceans) were merged with host trait data and IUCN Red List status to explore the distribution of single-host and multi-host parasites among threatened and non-threatened hosts. We find that threatened ungulates harbour a higher proportion of single-host parasites compared to non-threatened ungulates, which is explained by decreases in the richness of multi-host parasites. However, among carnivores threat status is not a significant predictor of the proportion of single-host parasites, or the richness of single-host or multi-host parasites. The loss of multi-host parasites from threatened ungulates may be explained by decreased cross-species contact as hosts decline and habitats become fragmented. Among carnivores, threat status may not be important in predicting patterns of parasite specificity because host decline results in equal losses of both single-host parasites and multi-host parasites through reduction in average population density and frequency of cross-species contact. Our results contrast with current models of parasite coextinction and highlight the need for updated theories that are applicable across host groups and account for both inter- and intraspecific contact. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Size Evolution and Stochastic Models: Explaining Ostracod Size through Probabilistic Distributions

NASA Astrophysics Data System (ADS)

Krawczyk, M.; Decker, S.; Heim, N. A.; Payne, J.

2014-12-01

The biovolume of animals has functioned as an important benchmark for measuring evolution throughout geologic time. In our project, we examined the observed average body size of ostracods over time in order to understand the mechanism of size evolution in these marine organisms. The body size of ostracods has varied since the beginning of the Ordovician, where the first true ostracods appeared. We created a stochastic branching model to create possible evolutionary trees of ostracod size. Using stratigraphic ranges for ostracods compiled from over 750 genera in the Treatise on Invertebrate Paleontology, we calculated overall speciation and extinction rates for our model. At each timestep in our model, new lineages can evolve or existing lineages can become extinct. Newly evolved lineages are assigned sizes based on their parent genera. We parameterized our model to generate neutral and directional changes in ostracod size to compare with the observed data. New sizes were chosen via a normal distribution, and the neutral model selected new sizes differentials centered on zero, allowing for an equal chance of larger or smaller ostracods at each speciation. Conversely, the directional model centered the distribution on a negative value, giving a larger chance of smaller ostracods. Our data strongly suggests that the overall direction of ostracod evolution has been following a model that directionally pushes mean ostracod size down, shying away from a neutral model. Our model was able to match the magnitude of size decrease. Our models had a constant linear decrease while the actual data had a much more rapid initial rate followed by a constant size. The nuance of the observed trends ultimately suggests a more complex method of size evolution. In conclusion, probabilistic methods can provide valuable insight into possible evolutionary mechanisms determining size evolution in ostracods.

Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction.

PubMed

Beaulieu, Jeremy M; O'Meara, Brian C

2016-07-01

The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Warning times for species extinctions due to climate change.

PubMed

Stanton, Jessica C; Shoemaker, Kevin T; Pearson, Richard G; Akçakaya, H Resit

2015-03-01

Climate change is likely to become an increasingly major obstacle to slowing the rate of species extinctions. Several new assessment approaches have been proposed for identifying climate-vulnerable species, based on the assumption that established systems such as the IUCN Red List need revising or replacing because they were not developed to explicitly consider climate change. However, no assessment approach has been tested to determine its ability to provide advanced warning time for conservation action for species that might go extinct due to climate change. To test the performance of the Red List system in this capacity, we used linked niche-demographic models with habitat dynamics driven by a 'business-as-usual' climate change scenario. We generated replicate 100-year trajectories for range-restricted reptiles and amphibians endemic to the United States. For each replicate, we categorized the simulated species according to IUCN Red List criteria at annual, 5-year, and 10-year intervals (the latter representing current practice). For replicates that went extinct, we calculated warning time as the number of years the simulated species was continuously listed in a threatened category prior to extinction. To simulate data limitations, we repeated the analysis using a single criterion at a time (disregarding other listing criteria). Results show that when all criteria can be used, the Red List system would provide several decades of warning time (median = 62 years; >20 years for 99% of replicates), but suggest that conservation actions should begin as soon as a species is listed as Vulnerable, because 50% of replicates went extinct within 20 years of becoming uplisted to Critically Endangered. When only one criterion was used, warning times were substantially shorter, but more frequent assessments increased the warning time by about a decade. Overall, we found that the Red List criteria reliably provide a sensitive and precautionary way to assess extinction risk under climate change. © 2014 John Wiley & Sons Ltd.

New records of Coccinellidae (Coleoptera) from Wyoming, U.S.A.

USDA-ARS?s Scientific Manuscript database

Faunal distributions are dynamic, and the fauna associated with a particular area may change due to accidental or intentional introductions of new species, extinctions, and natural geographic range expansions or contractions of species. Thus, periodic field surveys and collections of fauna are nece...

The Maintenance of Single-Locus Polymorphism. IV. Models with Mutation from Existing Alleles

PubMed Central

Spencer, H. G.; Marks, R. W.

1992-01-01

The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory. PMID:1732162

Beyond the pleistocene: using phylogeny and constraint to inform the evolutionary psychology of human mating.

PubMed

Eastwick, Paul W

2009-09-01

Evolutionary psychologists explore the adaptive function of traits and behaviors that characterize modern Homo sapiens. However, evolutionary psychologists have yet to incorporate the phylogenetic relationship between modern Homo sapiens and humans' hominid and pongid relatives (both living and extinct) into their theorizing. By considering the specific timing of evolutionary events and the role of evolutionary constraint, researchers using the phylogenetic approach can generate new predictions regarding mating phenomena and derive new explanations for existing evolutionary psychological findings. Especially useful is the concept of the adaptive workaround-an adaptation that manages the maladaptive elements of a pre-existing evolutionary constraint. The current review organizes 7 features of human mating into their phylogenetic context and presents evidence that 2 adaptive workarounds played a critical role as Homo sapiens's mating psychology evolved. These adaptive workarounds function in part to mute or refocus the effects of older, previously evolved adaptations and highlight the layered nature of humans' mating psychology. (c) 2009 APA, all rights reserved.

Tempo of trophic evolution and its impact on mammalian diversification

PubMed Central

Price, Samantha A.; Hopkins, Samantha S. B.; Smith, Kathleen K.; Roth, V. Louise

2012-01-01

Mammals are characterized by the complex adaptations of their dentition, which are an indication that diet has played a critical role in their evolutionary history. Although much attention has focused on diet and the adaptations of specific taxa, the role of diet in large-scale diversification patterns remains unresolved. Contradictory hypotheses have been proposed, making prediction of the expected relationship difficult. We show that net diversification rate (the cumulative effect of speciation and extinction), differs significantly among living mammals, depending upon trophic strategy. Herbivores diversify fastest, carnivores are intermediate, and omnivores are slowest. The tempo of transitions between the trophic strategies is also highly biased: the fastest rates occur into omnivory from herbivory and carnivory and the lowest transition rates are between herbivory and carnivory. Extant herbivore and carnivore diversity arose primarily through diversification within lineages, whereas omnivore diversity evolved by transitions into the strategy. The ability to specialize and subdivide the trophic niche allowed herbivores and carnivores to evolve greater diversity than omnivores. PMID:22509033

Tempo of trophic evolution and its impact on mammalian diversification.

PubMed

Price, Samantha A; Hopkins, Samantha S B; Smith, Kathleen K; Roth, V Louise

2012-05-01

Mammals are characterized by the complex adaptations of their dentition, which are an indication that diet has played a critical role in their evolutionary history. Although much attention has focused on diet and the adaptations of specific taxa, the role of diet in large-scale diversification patterns remains unresolved. Contradictory hypotheses have been proposed, making prediction of the expected relationship difficult. We show that net diversification rate (the cumulative effect of speciation and extinction), differs significantly among living mammals, depending upon trophic strategy. Herbivores diversify fastest, carnivores are intermediate, and omnivores are slowest. The tempo of transitions between the trophic strategies is also highly biased: the fastest rates occur into omnivory from herbivory and carnivory and the lowest transition rates are between herbivory and carnivory. Extant herbivore and carnivore diversity arose primarily through diversification within lineages, whereas omnivore diversity evolved by transitions into the strategy. The ability to specialize and subdivide the trophic niche allowed herbivores and carnivores to evolve greater diversity than omnivores.

A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein

PubMed Central

Rodriguez, Erik A.; Tran, Geraldine N.; Gross, Larry A.; Crisp, Jessica L.; Shu, Xiaokun; Lin, John Y.; Tsien, Roger Y.

2016-01-01

Far-red fluorescent proteins (FPs) are desirable for in vivo imaging because less light is scattered, absorbed, or reemitted by endogenous biomolecules. A new class of FP was developed from an allophycocyanin α-subunit (APCα). Native APC requires a lyase to incorporate phycocyanobilin. The evolved FP, named small Ultra-Red FP (smURFP), covalently attaches biliverdin (BV) without a lyase, and has 642/670 nm excitation/emission peaks, a large extinction coefficient (180,000 M−1cm−1) and quantum yield (18%), and comparable photostability to eGFP. SmURFP has significantly increased BV incorporation rate and protein stability compared to the bacteriophytochrome (BPH) FPs. BV supply is limited by membrane permeability, so expression of heme oxygenase-1 with heme precursors increases fluorescence of BPH/APCα FPs. SmURFP (but not BPH FPs) can incorporate a more membrane-permeant BV analog, making smURFP fluorescence in situ comparable to FPs from jellyfish/coral. A far-red/near-infrared fluorescent cell cycle indicator was created with smURFP and a BPH FP. PMID:27479328

Analyzing nature's protective design: The glyptodont body armor.

PubMed

du Plessis, Anton; Broeckhoven, Chris; Yadroitsev, Igor; Yadroitsava, Ina; le Roux, Stephan Gerhard

2018-06-01

Many animal species evolved some form of body armor, such as scales of fish and bony plates or osteoderms of reptiles. Although a protective function is often taken for granted, recent studies show that body armor might comprise multiple functionalities and is shaped by trade-offs among these functionalities. Hence, despite the fact that natural body armor might serve as bio-inspiration for the development of artificial protective materials, focussing on model systems in which body armor serves a solely protective function might be pivotal. In this study, we investigate the osteoderms of Glyptotherium arizonae, an extinct armadillo-like mammal in which body armor evolved as protection against predators and/or tail club blows of conspecifics. By using a combination of micro-computed tomography, reverse-engineering, stress simulations and mechanical testing of 3D printed models, we show that the combination of dense compact layers and porous lattice core might provide an optimized combination of strength and high energy absorption. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night.

PubMed

Liow, Lee Hsiang; Reitan, Trond; Harnik, Paul G

2015-10-01

Competition among organisms has ecological and evolutionary consequences. However, whether the consequences of competition are manifested and measureable on macroevolutionary time scales is equivocal. Marine bivalves and brachiopods have overlapping niches such that competition for food and space may occur. Moreover, there is a long-standing debate over whether bivalves outcompeted brachiopods evolutionarily, because brachiopod diversity declined through time while bivalve diversity increased. To answer this question, we estimate the origination and extinction dynamics of fossil marine bivalve and brachiopod genera from the Ordovician through to the Recent while simultaneously accounting for incomplete sampling. Then, using stochastic differential equations, we assess statistical relationships among diversification and sampling dynamics of brachiopods and bivalves and five paleoenvironmental proxies. None of these potential environmental drivers had any detectable influence on brachiopod or bivalve diversification. In contrast, elevated bivalve extinction rates causally increased brachiopod origination rates, suggesting that bivalves have suppressed brachiopod evolution. © 2015 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Flame extinction limit and particulates formation in fuel blends

NASA Astrophysics Data System (ADS)

Subramanya, Mahesh

Many fuels used in material processing and power generation applications are generally a blend of various hydrocarbons. Although the combustion and aerosol formation dynamics of individual fuels is well understood, the flame dynamics of fuel blends are yet to be characterized. This research uses a twin flame counterflow burner to measure flame velocity, flame extinction, particulate formation and particulate morphology of hydrogen fuel blend flames at different H2 concentration, oscillation frequencies and stretch conditions. Phase resolved spectroscopic measurements (emission spectra) of OH, H, O and CH radical/atom concentrations is used to characterize the heat release processes of the flame. In addition flame generated particulates are collected using thermophoretic sample technique and are qualitative analyzed using Raman Spectroscopy and SEM. Such measurements are essential for the development of advanced computational tools capable of predicting fuel blend flame characteristics at realistic combustor conditions. The data generated through the measurements of this research are representative, and yet accurate, with unique well defined boundary conditions which can be reproduced in numerical computations for kinetic code validations.

Critical Slowing Down in Time-to-Extinction: An Example of Critical Phenomena in Ecology

NASA Technical Reports Server (NTRS)

Gandhi, Amar; Levin, Simon; Orszag, Steven

1998-01-01

We study a model for two competing species that explicitly accounts for effects due to discreteness, stochasticity and spatial extension of populations. The two species are equally preferred by the environment and do better when surrounded by others of the same species. We observe that the final outcome depends on the initial densities (uniformly distributed in space) of the two species. The observed phase transition is a continuous one and key macroscopic quantities like the correlation length of clusters and the time-to-extinction diverge at a critical point. Away from the critical point, the dynamics can be described by a mean-field approximation. Close to the critical point, however, there is a crossover to power-law behavior because of the gross mismatch between the largest and smallest scales in the system. We have developed a theory based on surface effects, which is in good agreement with the observed behavior. The course-grained reaction-diffusion system obtained from the mean-field dynamics agrees well with the particle system.

PHIBSS: MOLECULAR GAS, EXTINCTION, STAR FORMATION, AND KINEMATICS IN THE z = 1.5 STAR-FORMING GALAXY EGS13011166

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genzel, R.; Tacconi, L. J.; Kurk, J.

We report matched resolution imaging spectroscopy of the CO 3-2 line (with the IRAM Plateau de Bure millimeter interferometer) and of the H{alpha} line (with LUCI at the Large Binocular Telescope) in the massive z = 1.53 main-sequence galaxy EGS 13011166, as part of the ''Plateau de Bure high-z, blue-sequence survey'' (PHIBSS: Tacconi et al.). We combine these data with Hubble Space Telescope V-I-J-H-band maps to derive spatially resolved distributions of stellar surface density, star formation rate, molecular gas surface density, optical extinction, and gas kinematics. The spatial distribution and kinematics of the ionized and molecular gas are remarkably similarmore » and are well modeled by a turbulent, globally Toomre unstable, rotating disk. The stellar surface density distribution is smoother than the clumpy rest-frame UV/optical light distribution and peaks in an obscured, star-forming massive bulge near the dynamical center. The molecular gas surface density and the effective optical screen extinction track each other and are well modeled by a ''mixed'' extinction model. The inferred slope of the spatially resolved molecular gas to star formation rate relation, N = dlog{Sigma}{sub starform}/dlog{Sigma}{sub molgas}, depends strongly on the adopted extinction model, and can vary from 0.8 to 1.7. For the preferred mixed dust-gas model, we find N = 1.14 {+-} 0.1.« less

Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes.

PubMed

Betancur-R, Ricardo; Ortí, Guillermo; Pyron, Robert Alexander

2015-05-01

The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies. © 2015 John Wiley & Sons Ltd/CNRS.

Testing the adaptive radiation hypothesis for the lemurs of Madagascar.

PubMed

Herrera, James P

2017-01-01

Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an 'early burst' of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the 'early burst' signal of adaptive radiation may have been eroded by extinction.

Periodic mass extinctions and the Planet X model reconsidered

NASA Astrophysics Data System (ADS)

Whitmire, Daniel P.

2016-01-01

The 27 Myr period in the fossil extinction record has been confirmed in modern data bases dating back 500 Myr, which is twice the time interval of the original analysis from 30 years ago. The surprising regularity of this period has been used to reject the Nemesis model. A second model based on the Sun's vertical Galactic oscillations has been challenged on the basis of an inconsistency in period and phasing. The third astronomical model originally proposed to explain the periodicity is the Planet X model in which the period is associated with the perihelion precession of the inclined orbit of a trans-Neptunian planet. Recently, and unrelated to mass extinctions, a trans-Neptunian super-Earth planet has been proposed to explain the observation that the inner Oort cloud objects Sedna and 2012VP113 have perihelia that lie near the ecliptic plane. In this Letter, we reconsider the Planet X model in light of the confluence of the modern palaeontological and outer Solar system dynamical evidence.

Persistence versus extinction for a class of discrete-time structured population models.

PubMed

Jin, Wen; Smith, Hal L; Thieme, Horst R

2016-03-01

We provide sharp conditions distinguishing persistence and extinction for a class of discrete-time dynamical systems on the positive cone of an ordered Banach space generated by a map which is the sum of a positive linear contraction A and a nonlinear perturbation G that is compact and differentiable at zero in the direction of the cone. Such maps arise as year-to-year projections of population age, stage, or size-structure distributions in population biology where typically A has to do with survival and individual development and G captures the effects of reproduction. The threshold distinguishing persistence and extinction is the principal eigenvalue of (II−A)(−1)G'(0) provided by the Krein-Rutman Theorem, and persistence is described in terms of associated eigenfunctionals. Our results significantly extend earlier persistence results of the last two authors which required more restrictive conditions on G. They are illustrated by application of the results to a plant model with a seed bank.

Testing the adaptive radiation hypothesis for the lemurs of Madagascar

PubMed Central

2017-01-01

Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an ‘early burst’ of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the ‘early burst’ signal of adaptive radiation may have been eroded by extinction. PMID:28280597

A System Computational Model of Implicit Emotional Learning

PubMed Central

Puviani, Luca; Rama, Sidita

2016-01-01

Nowadays, the experimental study of emotional learning is commonly based on classical conditioning paradigms and models, which have been thoroughly investigated in the last century. Unluckily, models based on classical conditioning are unable to explain or predict important psychophysiological phenomena, such as the failure of the extinction of emotional responses in certain circumstances (for instance, those observed in evaluative conditioning, in post-traumatic stress disorders and in panic attacks). In this manuscript, starting from the experimental results available from the literature, a computational model of implicit emotional learning based both on prediction errors computation and on statistical inference is developed. The model quantitatively predicts (a) the occurrence of evaluative conditioning, (b) the dynamics and the resistance-to-extinction of the traumatic emotional responses, (c) the mathematical relation between classical conditioning and unconditioned stimulus revaluation. Moreover, we discuss how the derived computational model can lead to the development of new animal models for resistant-to-extinction emotional reactions and novel methodologies of emotions modulation. PMID:27378898

A System Computational Model of Implicit Emotional Learning.

PubMed

Puviani, Luca; Rama, Sidita

2016-01-01

Nowadays, the experimental study of emotional learning is commonly based on classical conditioning paradigms and models, which have been thoroughly investigated in the last century. Unluckily, models based on classical conditioning are unable to explain or predict important psychophysiological phenomena, such as the failure of the extinction of emotional responses in certain circumstances (for instance, those observed in evaluative conditioning, in post-traumatic stress disorders and in panic attacks). In this manuscript, starting from the experimental results available from the literature, a computational model of implicit emotional learning based both on prediction errors computation and on statistical inference is developed. The model quantitatively predicts (a) the occurrence of evaluative conditioning, (b) the dynamics and the resistance-to-extinction of the traumatic emotional responses, (c) the mathematical relation between classical conditioning and unconditioned stimulus revaluation. Moreover, we discuss how the derived computational model can lead to the development of new animal models for resistant-to-extinction emotional reactions and novel methodologies of emotions modulation.

Fish community reassembly after a coral mass mortality: higher trophic groups are subject to increased rates of extinction.

PubMed

Alonso, David; Pinyol-Gallemí, Aleix; Alcoverro, Teresa; Arthur, Rohan

2015-05-01

Since Gleason and Clements, our understanding of community dynamics has been influenced by theories emphasising either dispersal or niche assembly as central to community structuring. Determining the relative importance of these processes in structuring real-world communities remains a challenge. We tracked reef fish community reassembly after a catastrophic coral mortality in a relatively unfished archipelago. We revisited the stochastic model underlying MacArthur and Wilson's Island Biogeography Theory, with a simple extension to account for trophic identity. Colonisation and extinction rates calculated from decadal presence-absence data based on (1) species neutrality, (2) trophic identity and (3) site-specificity were used to model post-disturbance reassembly, and compared with empirical observations. Results indicate that species neutrality holds within trophic guilds, and trophic identity significantly increases overall model performance. Strikingly, extinction rates increased clearly with trophic position, indicating that fish communities may be inherently susceptible to trophic downgrading even without targeted fishing of top predators. © 2015 John Wiley & Sons Ltd/CNRS.

High population variability and source-sink dynamics in a solitary bee species.

PubMed

Franzén, Markus; Nilsson, Sven G

2013-06-01

Although solitary bees are considered to play key roles in ecosystem functions, surprisingly few studies have explored their population dynamics. We investigated the population dynamics of a rare, declining, solitary bee (Andrena humilis) in a landscape of 80 km2 in southern Sweden from 2003 to 2011. Only one population was persistent throughout all years studied; most likely this population supplied the surrounding landscape with 11 smaller, temporary local populations. Despite stable pollen availability, the size of the persistent population fluctuated dramatically in a two-year cycle over the nine years, with 490-1230 nests in odd-numbered years and 21-48 nests in even-numbered years. These fluctuations were not significantly related to climatic variables or pollen availability. Nineteen colonization and 14 extinction events were recorded. Occupancy decreased with distance from the persistent population and increased with increasing resource (pollen) availability. There were significant positive correlations between the size of the persistent population and patch occupancy and colonization. Colonizations were generally more common in patches closer to the persistent population, whereas extinctions were independent of distance from the persistent population. Our results highlight the complex population dynamics that exist for this solitary bee species, which could be due to source-sink dynamics, a prolonged diapause, or can represent a bet-hedging strategy to avoid natural enemies and survive in small habitat patches. If large fluctuations in solitary bee populations prove to be widespread, it will have important implications for interpreting ecological relationships, bee conservation, and pollination.

Regime shifts and ecological catastrophes in a model of plankton-oxygen dynamics under the climate change.

PubMed

Petrovskii, Sergei; Sekerci, Yadigar; Venturino, Ezio

2017-07-07

It is estimated that more than a half of the total atmospheric oxygen is produced in the oceans due to the photosynthetic activity of phytoplankton. Any significant decrease in the net oxygen production by phytoplankton is therefore likely to result in the depletion of atmospheric oxygen and in a global mass mortality of animals and humans. In its turn, the rate of oxygen production is known to depend on water temperature and hence can be affected by the global warming. We address this problem theoretically by considering a model of a coupled plankton-oxygen dynamics where the rate of oxygen production slowly changes with time to account for the ocean warming. We show that, when the temperature rises sufficiently high, a regime shift happens: the sustainable oxygen production becomes impossible and the system's dynamics leads to fast oxygen depletion and plankton extinction. We also consider a scenario when, after a certain period of increase, the temperature is set on a new higher yet apparently safe value, i.e. before the oxygen depletion disaster happens. We show that in this case the system dynamics may exhibit a long-term quasi-sustainable dynamics that can still result in an ecological disaster (oxygen depletion and mass extinctions) but only after a considerable period of time. Finally, we discuss the early warning signals of the approaching regime shift resulting in the disaster. Copyright © 2017 Elsevier Ltd. All rights reserved.

Volcanic Signatures in Estimates of Stratospheric Aerosol Size, Distribution Width, Surface Area, and Volume Deduced from Global Satellite-Based Observations

NASA Technical Reports Server (NTRS)

Bauman, J. J.; Russell, P. B.

2000-01-01

Volcanic signatures in the stratospheric aerosol layer are revealed by two independent techniques which retrieve aerosol information from global satellite-based observations of particulate extinction. Both techniques combine the 4-wavelength Stratospheric Aerosol and Gas Experiment (SAGE) II extinction measurements (0.385 <= lambda <= 1.02 microns) with the 7.96 micron and 12.82 micron extinction measurements from the Cryogenic Limb Array Etalon Spectrometer (CLAES) instrument. The algorithms use the SAGE II/CLAES composite extinction spectra in month-latitude-altitude bins to retrieve values and uncertainties of particle effective radius R(sub eff), surface area S, volume V and size distribution width sigma(sub R). The first technique is a multi-wavelength Look-Up-Table (LUT) algorithm which retrieves values and uncertainties of R(sub eff) by comparing ratios of extinctions from SAGE II and CLAES (e.g., E(sub lambda)/E(sub 1.02) to pre-computed extinction ratios which are based on a range of unimodal lognormal size distributions. The pre-computed ratios are presented as a function of R(sub eff) for a given sigma(sub g); thus the comparisons establish the range of R(sub eff) consistent with the measured spectra for that sigma(sub g). The fact that no solutions are found for certain sigma(sub g) values provides information on the acceptable range of sigma(sub g), which is found to evolve in response to volcanic injections and removal periods. Analogous comparisons using absolute extinction spectra and error bars establish the range of S and V. The second technique is a Parameter Search Technique (PST) which estimates R(sub eff) and sigma(sub g) within a month-latitude-altitude bin by minimizing the chi-squared values obtained by comparing the SAGE II/CLAES extinction spectra and error bars with spectra calculated by varying the lognormal fitting parameters: R(sub eff), sigma(sub g), and the total number of particles N(sub 0). For both techniques, possible biases in retrieved-parameters caused by assuming a unimodal functional form are removed using correction factors computed from representative in situ measurements of bimodal size distributions. Some interesting features revealed by the LUT and PST retrievals include: (1) Increases in S and V (but not R(sub eff)) after the Ruiz and Kelut injections, (2) Increases in S, V, R(sub eff) after Pinatubo, (3) Post-Pinatubo increases in S, V, and R(sub eff) that are more rapid in the tropics than elsewhere, (4) Mid-latitude post-Pinatubo increases in R(sub eff) that lag increases in S and V, (5) S and V returning to pre-Pinatubo values sooner than R(sub eff) does, (6) Sharp increases in sigma(sub g), after Pinatubo and slight increases in sigma(sub g) after Ruiz, Etna, Kelut, Spurr and Rabaul, and (7) Gradual declines in the heights at which R(sub eff), S and V peak after Pinatubo.

Dynamic model of time-dependent complex networks.

PubMed

Hill, Scott A; Braha, Dan

2010-10-01

The characterization of the "most connected" nodes in static or slowly evolving complex networks has helped in understanding and predicting the behavior of social, biological, and technological networked systems, including their robustness against failures, vulnerability to deliberate attacks, and diffusion properties. However, recent empirical research of large dynamic networks (characterized by irregular connections that evolve rapidly) has demonstrated that there is little continuity in degree centrality of nodes over time, even when their degree distributions follow a power law. This unexpected dynamic centrality suggests that the connections in these systems are not driven by preferential attachment or other known mechanisms. We present an approach to explain real-world dynamic networks and qualitatively reproduce these dynamic centrality phenomena. This approach is based on a dynamic preferential attachment mechanism, which exhibits a sharp transition from a base pure random walk scheme.

High School Environmental Science Course Guide.

ERIC Educational Resources Information Center

Donovan, Edward P.; Korman, Barbara

A course in environmental science was developed to increase course options for students of all abilities and interest levels. Major topic areas of the course include: introduction to ecological principles and ecosystems; extinction of species; human population dynamics; agricultural systems and pest control; air quality; water quality; solid…