CiteULike: Tag ecology

The co-evolutionary genetics of ecological communities

Michael Wade — 2007-02-17T21:01:12-00:00

Nature Reviews Genetics, Vol. 8, No. 3. (06 February 2007), pp. 185-195.

Using pyrosequencing to shed light on deep mine microbial ecology.

RA Edwards — 2007-03-08T04:04:08-00:00

BMC Genomics, Vol. 7 (2006)

BACKGROUND: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology. RESULTS: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date. CONCLUSION: We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer

Christopher Bagwell — 2006-06-20T13:44:44-00:00

FEMS Microbiology Ecology, Vol. 55, No. 3. (2006), pp. 424-431.

Abstract The impact of legacy nuclear waste on the compositional diversity and distribution of sulfate-reducing bacteria in a heavily contaminated subsurface aquifer was examined. dsrAB clone libraries were constructed and restriction fragment length polymorphism (RFLP) analysis used to evaluate genetic variation between sampling wells. Principal component analysis identified nickel, nitrate, technetium, and organic carbon as the primary variables contributing to well-to-well geochemical variability, although comparative sequence analysis showed the sulfate-reducing bacteria community structure to be consistent throughout contaminated and uncontaminated regions of the aquifer. Only 3% of recovered dsrAB gene sequences showed apparent membership to the Deltaproteobacteria. The remainder of recovered sequences may represent novel, deep-branching lineages that, to our knowledge, do not presently contain any cultivated members; although corresponding phylotypes have recently been reported from several different marine ecosystems. These findings imply resiliency and adaptability of sulfate-reducing bacteria to extremes in environmental conditions, although the possibility for horizontal transfer of dsrAB is also discussed.

Predicting the ecological consequences of environmental change: a review of the methods

William Sutherland — 2006-06-26T20:18:26-00:00

Journal of Applied Ecology, Vol. 43, No. 4. (August 2006), pp. 599-616.

The identification of 100 ecological questions of high policy relevance in the UK

William Sutherland — 2006-06-26T20:18:25-00:00

Journal of Applied Ecology, Vol. 43, No. 4. (August 2006), pp. 617-627.

Prolonged clonal growth: escape route or route to extinction?

Olivier Honnay — 2004-12-28T16:16:12-00:00

Oikos, Vol. 108, No. 2., 427.

Adaptation of Evolutionary Agents in Computational Ecologies

Paul Devine — 2006-05-29T11:03:11-00:00

(1997), pp. 66-75.

. We present a system developed for the application of evolutionary computation techniques to ecological simulation. A model ecosystem comprised of discrete adaptive agents and a biologically inspired environment is described and results presented. The agents are classifier based animats and the overall system has been derived from real ecologies and interactions. 1 Introduction Ecologies are extremely complex biological systems in which adaptation is an essential characteristic. This operates ...

Tracking the ecological overshoot of the human economy

Mathis Wackernagel — 2006-10-12T10:10:43-00:00

Proceedings of the National Academy of Sciences USA, Vol. 99, No. 14. (9 July 2002), pp. 9266-9271.

Sustainability requires living within the regenerative capacity of the biosphere. In an attempt to measure the extent to which humanity satisfies this requirement, we use existing data to translate human demand on the environment into the area required for the production of food and other goods, together with the absorption of wastes. Our accounts indicate that human demand may well have exceeded the biosphere's regenerative capacity since the 1980s. According to this preliminary and exploratory assessment, humanity's load corresponded to 70% of the capacity of the global biosphere in 1961, and grew to 120% in 1999. 10.1073/pnas.142033699

Reproductive ecology of Aquilaria spp. in Indonesia

Tonny Soehartono — 2007-02-19T15:57:14-00:00

Forest Ecology and Management, Vol. 152, No. 1-3. (15 October 2001), pp. 59-71.

Aquilaria spp. (Thymelaeaceae) are the principal source of Gaharu, a valuable resin, yet information about their reproductive ecology is almost entirely lacking. Individuals of six species (A. beccariana, A. crasna, A. filaria, A. hirta, A. malaccensis and A. microcarpa) in cultivation in Indonesia were investigated to assess reproductive phenology, pollination, seed production and germination. Seed production and seedling dispersion were also assessed in natural populations of A. beccariana, A. malaccensis and A. microcarpa in Kalimantan. Most of the selected trees flowered during the dry season, fruits requiring between 36 and 72 days to develop, depending on the species. Twenty different species of insect were recorded visiting flowering trees. The probability of flowers developing into fruit varied between species from 0.04 to 0.43, although flowers from which pollinators were excluded never produced fruit. Seed production of A. malaccensis and A. microcarpa peaked at a dbh of approximately 40 and 50 cm, respectively, individual trees producing up to 19,000 seeds in a single season. Germination under nursery conditions was initiated 7-15 days after sowing; seeds of A. crasna had the highest probability of germination success (92%) whereas those of A. filaria had the lowest (53%). In natural forest, most seedlings (>65%) occurred within 5 m of an adult tree, suggesting limited dispersal. These results indicate that Aquilaria spp. have high reproductive potential, but suggest that seed dispersal might be limited in natural forests. The implications of these results for the management of Aquilaria spp. are discussed.

Impact of war on conservation: Rwandan environment and wildlife in agony

Samuel Kanyamibwa — 2007-02-19T13:53:30-00:00

Biodiversity and Conservation, Vol. V7, No. 11. (1 November 1998), pp. 1399-1406.

Among the crucial problems that affect conservation in less developed countries are the high human pressure on natural habitats, poverty, low conservation education and lack of integration of local population. However, political and ethnic conflicts, which occur around the world and particularly in African countries, significantly affect all sectors of human society, the environment and wildlife. In this paper, we discuss the consequences of the Rwandan civil war of 1990–1994, recognized as one of the major tragedies of the 20th century, with a particular focus on protected areas and conservation bodies in the country.

Simulating Chemosensory Responses of Marine Microorganisms

George Jackson — 2007-10-30T19:16:33-00:00

Limnology and Oceanography, Vol. 32, No. 6. (1987), pp. 1253-1266.

I have studied the nature of chemosensory interactions in situations relevant to aquatic ecosystems by incorporating a model of chemokinesis by laboratory bacteria into a Monte Carlo simulation of bacterial movement around leaky microalgae. I assumed that the concentration field of the substrate around an alga is determined by molecular diffusion. Results of simulations and various theoretical arguments imply that there is a smallest organism size with a radius > 2 μm which bacteria can find using chemosensory responses. Bacteria most easily find algae that are large and have a high specific leakage rate. Because its feeding also involves chemosensing of food items, a copepod's observed inability to feed on small algae may also be the result of its inability to sense this potential food. The lack of sensory mechanisms to detect small organisms at a distance implies that the sensing of small organisms must, by default, involve physical contact. This inference agrees with filtration mechanisms noted for microzooplankton feeding.

Role of motility, chemotaxis, and adhesion in microbial ecology

MJ Kennedy — 2008-04-16T13:09:54-00:00

Ann NY Acad Sci, Vol. 506, No. 1. (2 January 1987), pp. 260-273.

Quantitative studies of bacterial chemotaxis and microbial population dynamics

Douglas Lauffenburger — 2008-04-16T12:49:54-00:00

Microbial Ecology, Vol. 22, No. 1. (5 December 1991), pp. 175-185.

Abstract Although there is a long history of conjecture regarding the role and significance of bacterial chemotaxis in microbial ecology, only recently has a significant body of work appeared attempting to address this issue. The purpose of this paper is to provide a concise overview of this work, which combined mathematical modeling of bacterial population migration and experimental measurement of the model parameters with modeling of competitive microbial population dynamics in a nonmixed environment. Predictions from the population dynamics models, based on experimental estimates of the various motility and growth parameter values, are related to the small number of experimental observations available to date dealing with the effects of bacterial motility on competition in a nonmixed environment. Current results indicate that cell motility and chemotaxis properties can be as important to population dynamics as cell growth kinetic properties, so that greater attention to this aspect of microbial behavior is warranted in future studies of microbial ecology.

Multidecadal trends for three declining fish species: habitat patterns and mechanisms in the San Francisco Estuary, California, USA

Frederick Feyrer — 2008-04-23T23:51:37-00:00

Canadian Journal of Fisheries and Aquatic Sciences (April 2007), pp. 723-734.

We examined a 36-year record of concurrent midwater trawl and water quality sampling conducted during fall to evaluate habitat trends for three declining fish species in the San Francisco Estuary, California, USA: delta smelt (Hypomesus transpacificus), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). Generalized additive modeling revealed that Secchi depth and specific conductance were important predictors of occurrence for delta smelt and striped bass, while specific conductance and water temperature were important for threadfin shad. Habitat suitability derived from model predictions exhibited significant long-term declines for each species; the southeastern and western regions of the estuary exhibited the most dramatic changes. Declines in habitat suitability were associated with anthropogenic modifications to the ecosystem. For delta smelt, an imperiled annual species endemic to the estuary, the combined effects of fall stock abundance and water quality predicted recruit abundance during recent years of chronically low food supply. Our results are consistent with existing evidence of a long-term decline in carrying capacity for delta smelt and striped bass and demonstrate the utility of long-term data sets for evaluating relationships between fish and their habitat.Nous avons examiné des données concomitantes d'échantillonnage au chalut en pleine eau et d'échantillonnage de la qualité de l'eau faites à chaque automne pendant 36 années dans l'estuaire de San Francisco, Californie, É.-U., afin d'évaluer les tendances de l'habitat chez trois espèces de poissons en déclin, soit l'éperlan du delta (Hypomesus transpacificus), le bar rayé (Morone saxatilis) et l'alose fil (Dorosoma petenense). Un modèle additif généralisé montre que la profondeur de Secchi et la conductance spécifique sont d'importantes variables explicatives de la présence de l'éperlan du delta et du bar rayé, alors que la conductance spécifique et la température de l'eau le sont pour l'alose fil. Les prédictions du modèle indiquent une diminution significative à long terme de la qualité de l'habitat pour chaque espèce; les régions du sud-est et de l'ouest de l'estuaire montrent les changements les plus spectaculaires. Le déclin de la qualité de l'habitat est associé à des modifications anthropiques de l'écosystème. Chez l'éperlan du delta, une espèce annuelle, menacée et endémique à l'estuaire, les effets combinés de l'abondance des stocks à l'automne et de la qualité de l'eau expliquent l'abondance du recrutement durant les années récentes de sources de nourriture chroniquement limitées. Nos résultats confirment les indications existantes d'un déclin à long terme du stock limite de l'éperlan du delta et du bar rayé; ils démontrent l'utilité des banques de données couvrant de grandes périodes pour l'évaluation des relations entre les poissons et leur habitat.[Traduit par la Rédaction]

An ecological approach to embodiment and cognition

Naoya Hirose — 2005-04-24T04:48:52-00:00

Cognitive Systems Research, Vol. 3, No. 3. (September 2002), pp. 289-299.

The purpose of this article is to explore the relation between embodiment and cognition from an ecological point of view, which has been given little attention in current studies on embodiment. To begin with, two basic meanings of embodiment are distinguished: the state of being embodied and the act of embodying. This article gives more attention to embodying than to being embodied. Next, the ecological framework to investigate embodiment are presented, with focusing on affordances, tool use, and the body. On this view, it is argued that tools extend action and perception capabilities, which implies that the boundary of the body can be extended beyond the surface of the skin. Then, the empirical studies on perception of affordances, on limb proprioception, and on tool use are outlined. These studies support the idea that the boundary of the body can shift. Finally, the boundary of the body is discussed in reference to perception-action systems, suggesting that research on embodiment should pay more attention to the dynamic nature of the body.

Fitting Multivariate Models to Community Data: A Comment on Distance-Based Redundancy Analysis

Brian Mcardle — 2007-05-22T14:55:11-00:00

Ecology, Vol. 82, No. 1. (2001), pp. 290-297.

Nonparametric multivariate analysis of ecological data using permutation tests has two main challenges: (1) to partition the variability in the data according to a complex design or model, as is often required in ecological experiments, and (2) to base the analysis on a multivariate distance measure (such as the semimetric Bray-Curtis measure) that is reasonable for ecological data sets. Previous nonparametric methods have succeeded in one or other of these areas, but not in both. A recent contribution to Ecological Monographs by Legendre and Anderson, called distance-based redundancy analysis (db-RDA), does achieve both. It does this by calculating principal coordinates and subsequently correcting for negative eigenvalues, if they are present, by adding a constant to squared distances. We show here that such a correction is not necessary. Partitioning can be achieved directly from the distance matrix itself, with no corrections and no eigenanalysis, even if the distance measure used is semimetric. An ecological example is given to show the differences in these statistical methods. Empirical simulations, based on parameters estimated from real ecological species abundance data, showed that db-RDA done on multi-factorial designs (using the correction) does not have type 1 error consistent with the significance level chosen for the analysis (i.e., does not provide an exact test), whereas the direct method described and advocated here does.

Absence of detectable transgenes in local landraces of maize in Oaxaca, Mexico (2003-2004).

S Ortiz-García — 2005-09-11T19:50:08-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 35. (30 August 2005), pp. 12338-12343.

In 2000, transgenes were detected in local maize varieties (landraces) in the mountains of Oaxaca, Mexico [Quist, D. & Chapela, I. H. (2001) Nature 414, 541-543]. This region is part of the Mesoamerican center of origin for maize (Zea mays L.), and the genetic diversity that is maintained in open-pollinated landraces is recognized as an important genetic resource of great cultural value. The presence of transgenes in landraces was significant because transgenic maize has never been approved for cultivation in Mexico. Here we provide a systematic survey of the frequency of transgenes in currently grown landraces. We sampled maize seeds from 870 plants in 125 fields and 18 localities in the state of Oaxaca during 2003 and 2004. We then screened 153,746 sampled seeds for the presence of two transgene elements from the 35S promoter of the cauliflower mosaic virus and the nopaline synthase gene (nopaline synthase terminator) from Agrobacterium tumefaciens. One or both of these transgene elements are present in all transgenic commercial varieties of maize. No transgenic sequences were detected with highly sensitive PCR-based markers, appropriate positive and negative controls, and duplicate samples for DNA extraction. We conclude that transgenic maize seeds were absent or extremely rare in the sampled fields. This study provides a much-needed preliminary baseline for understanding the biological, socioeconomic, and ethical implications of the inadvertent dispersal of transgenes from the United States and elsewhere to local landraces of maize in Mexico.

The Tragedy of the Commons

Garrett Hardin — 2005-12-12T12:42:45-00:00

Science, Vol. 162, No. 3859. (13 December 1968), pp. 1243-1248.

The Political Economy of the Ecological Native

Molly Doane — 2007-10-09T07:22:10-00:00

American Anthropologist, Vol. 109, No. 3. (2007), pp. 452-462.

In Chimalapas, Mexico, nongovernmental actors attempted to integrate campesinos into the discourse and practices of the Western environmental movement. The political economy school of anthropology assumes that cultural identity and practice flow from historical experiences grounded in relevant national and institutional contexts. In this article, I argue that although the movement in Chimalapas drew from the well-developed symbolic toolkit of the environmental movement, it was not able to create a space for local concerns within a transnational agenda that was already fairly well established and inflexible. Political ecology was the hinge of this movement: a political-economic analysis that validated traditional agrarian concerns in Chimalapas but included an environmentalist discourse legible to international funders. In this way, environmentalists in Chimalapas attempted both to create new practices and to link old practices to new expressions of culture and identity.

Post-Scarcity Anarchism (Working Classics)

Murray Bookchin — 2007-06-25T15:03:50-00:00

(15 November 2004)

In this series of essays, Murray Bookchin balances his ecological and anarchist vision with the promising opportunities of a "post-scarcity" era. Technological advances during the 20th century have expanded production in the pursuit of corporate profit at the expense of human need and ecological sustainability. New possibilities for human freedom must combine an ecological outlook with the dissolution of hierarchical social relations, capitalism and canonical political orientation. Bookchin's utopian vision, rooted in the realities of contemporary society, remains refreshingly pragmatic. "Book-chin makes a trenchant analysis of modern society and offers a pointed, provocative discussion of the ecological crisis."-Library JournalMurray Bookchin has been an active voice in the ecology and anarchist movements for more than 40 years.

The ecological and consumption themes of the films of Hayao Miyazaki

Kozo Mayumi — 2008-06-26T22:09:42-00:00

Ecological Economics, Vol. 54, No. 1. (1 July 2005), pp. 1-7.

Films are an underutilized media to explore and amplify the many messages of ecological economics. While a few popular films and videos have effectively addressed environmental themes, this commentary argues that they have an even greater role to play in the educational process in order to reach a broader audience and help it to rethink its role in the world's ecosystems. Hayao Miyazaki, the masterful animator from Japan, is singled out to offer ample material in many of his popular and children's films to stimulate such critical thinking on the systemic problems addressed by ecological economics.

The Death of Smokey Bear: The Ecodisaster Myth and Forest Management Practices in Prehistoric North America

Roberta Dods — 2008-06-27T23:21:26-00:00

World Archaeology, Vol. 33, No. 3. (2002), pp. 475-487.

Through time primeval Europe was transformed into a landscape where managed woodlands (forestis) became repositories for resources and wild woods (silva) were seen as being occupied by wild men, the savages. The importation into the New World of these attitudes resulted in verdant North America being classified as 'wilderness'. It was generally assumed that the worlds of the past were essentially unaltered by hunter-gatherer activities. By the twentieth century, forest management practices in North America, supported by the myth of the primeval past, encouraged old growth forests through fire suppression. The fallacy of the unmanaged forest of prehistory is now being challenged. In its place are put forward models of forests as managed sustainers of a wide range of resources. In such models, fire is an essential management tool, not an ecodisaster.

Virus population extinction via ecological traps

Dennehy — 2007-02-27T01:56:02-00:00

Ecology Letters, Vol. 10, No. 3. (March 2007), pp. 230-240.

ECOLOGY: How Do Roots Interact?

Hans de Kroon — 2007-12-07T14:06:27-00:00

Science, Vol. 318, No. 5856. (7 December 2007), pp. 1562-1563.

10.1126/science.1150726

The dynamical theory of coevolution: a derivation from stochastic ecological processes

Ulf Dieckmann — 2007-04-18T05:21:49-00:00

Journal of Mathematical Biology, Vol. 34, No. 5. (12 May 1996), pp. 579-612.

Introduction to this special issue on the application of spatial statistics to agriculture, ecology, and the environment

Urquhart — 2007-03-17T11:22:34-00:00

Environmental and Ecological Statistics, Vol. 14, No. 1. (March 2007), pp. 1-3.

Stochastic Spatial Models: A User's Guide to Ecological Applications

Richard Durrett — 2007-04-03T17:43:42-00:00

Philosophical Transactions: Biological Sciences, Vol. 343, No. 1305. (1994), pp. 329-350.

Spatial pattern, how it arises and how it is maintained, are central foci for ecological theory. In recent years, some attention has shifted from continuum models to spatially discrete analogues, which allow easy treatment of local stochastic effects and of non-local spatial influences. Many of these fall within the area of mathematics known as `interacting particle systems', which provides a body of results that facilitate the interpretation of the suite of simulation models that have been considered, and point towards future analyses. In this paper we review the basic mathematical literature. Three influential examples from the ecological literature are considered and placed within the general framework, which is shown to be a powerful one for the study of spatial ecological interactions.

The Importance of Being Discrete (and Spatial)

R Durrett — 2007-04-03T15:38:24-00:00

Theoretical Population Biology, Vol. 46, No. 3. (December 1994), pp. 363-394.

We consider and compare four approaches to modeling the dynamics of spatially distributed systems: mean field approaches (described by ordinary differential equations) in which every individual is considered to have equal probability of interacting with every other individual; patch models that group discrete individuals into patches without additional spatial structure; reaction-diffusion equations, in which infinitesimal individuals are distributed in space; and interacting particle systems, in which individuals are discrete and space is treated explicitly. We apply these four approaches to three examples of species interactions in spatially distributed populations and compare their predictions. Each represents different assumptions about the biology and hence a comparison among them has biological as well as modeling implications. In the first case all four approaches agree, in the second the spatial models disagree with the nonspatial ones, while in the third the stochastic models with discrete individuals disagree with the ones based on differential equations. We show further that the limiting reaction-diffusion equations associated with particle systems can have different qualitative behavior from those obtained by simply adding diffusion terms to mean field equations.

Spatial Autocorrelation and Autoregressive Models in Ecology

Jeremy Lichstein — 2007-03-28T20:31:37-00:00

Ecological Monographs, Vol. 72, No. 3. (2002), pp. 445-463.

Recognition and analysis of spatial autocorrelation has defined a new paradigm in ecology. Attention to spatial pattern can lead to insights that would have been otherwise overlooked, while ignoring space may lead to false conclusions about ecological relationships. We used Gaussian spatial autoregressive models, fit with widely available software, to examine breeding habitat relationships for three common Neotropical migrant songbirds in the southern Appalachian Mountains of North Carolina and Tennessee, USA. In preliminary models that ignored space, the abundance of all three species was correlated with both local- and landscape-scale habitat variables. These models were then modified to account for broadscale spatial trend (via trend surface analysis) and fine-scale autocorrelation (via an autoregressive spatial covariance matrix). Residuals from ordinary least squares regression models were autocorrelated, indicating that the assumption of independent errors was violated. In contrast, residuals from autoregressive models showed little spatial pattern, suggesting that these models were appropriate. The magnitude of habitat effects tended to decrease, and the relative importance of different habitat variables shifted when we incorporated broadscale and then fine-scale space into the analysis. The degree to which habitat effects changed when space was added to the models was roughly correlated with the amount of spatial structure in the habitat variables. Spatial pattern in the residuals from ordinary least squares models may result from failure to include or adequately measure autocorrelated habitat variables. In addition, contagious processes, such as conspecific attraction, may generate spatial patterns in species abundance that cannot be explained by habitat models. For our study species, spatial patterns in the ordinary least squares residuals suggest that a scale of 500-1000 m would be appropriate for investigating possible contagious processes.

Spatial autocorrelation in multi-scale land use models

KP Overmars — 2007-03-28T20:34:08-00:00

Ecological Modelling, Vol. 164, No. 2-3. (15 June 2003), pp. 257-270.

In several land use models statistical methods are being used to analyse spatial data. Land use drivers that best describe land use patterns quantitatively are often selected through (logistic) regression analysis. A problem using conventional statistical methods, like (logistic) regression, in spatial land use analysis is that these methods assume the data to be statistically independent. But, spatial land use data have the tendency to be dependent, a phenomenon known as spatial autocorrelation. Values over distance are more similar or less similar than expected for randomly associated pairs of observations. In this paper correlograms of the Moran's I are used to describe spatial autocorrelation for a data set of Ecuador. Positive spatial autocorrelation was detected in both dependent and independent variables, and it is shown that the occurrence of spatial autocorrelation is highly dependent on the aggregation level. The residuals of the original regression model also show positive autocorrelation, which indicates that the standard multiple linear regression model cannot capture all spatial dependency in the land use data. To overcome this, mixed regressive-spatial autoregressive models, which incorporate both regression and spatial autocorrelation, were constructed. These models yield residuals without spatial autocorrelation and have a better goodness-of-fit. The mixed regressive-spatial autoregressive model is statistically sound in the presence of spatially dependent data, in contrast with the standard linear model which is not. By using spatial models a part of the variance is explained by neighbouring values. This is a way to incorporate spatial interactions that cannot be captured by the independent variables. These interactions are caused by unknown spatial processes such as social relations and market effects.

Geostatistical Tools for Modeling and Interpreting Ecological Spatial Dependence

Richard Rossi — 2007-02-28T00:24:57-00:00

Ecological Monographs, Vol. 62, No. 2. (1992), pp. 277-314.

Geostatistics brings to ecology novel tools for the interpretation of spatial patterns of organisms, of the numerous environmental components with which they interact, and of the joint spatial dependence between organisms and their environment. The purpose of this paper is to use data from the ecological literature as well as from original research to provide a comprehensive and easily understood analysis of geostatistics' manner of modeling and methods. The traditional geostatistical tool, the variogram, a tool that is beginning to be used in ecology, is shown to provide an incomplete and misleading summary of spatial pattern when local means and variances change. Use of the non-ergodic covariance and correlogram provides a more effective description of lag-to-lag spatial dependence because the changing local means and variances are accounted for. Indicator transformations capture the spatial patterns of nominal ecological variables like gene frequencies and the presence/absence of an organism and of subgroups of a population like large or small individuals. Robust variogram measures are shown to be useful in data sets that contain many data outliers. Appropriate removal of outliers reveals latent spatial dependence and patterns. Cross-variograms, cross-covariances, and cross-correlograms define the joint spatial dependence between co-occurring organisms. The results of all of these analyses bring new insights into the spatial relations of organisms in their environment.

Crude Chronicles: Indigenous Politics, Multinational Oil, and Neoliberalism in Ecuador (American Encounters/Global Interactions)

Suzana Sawyer — 2008-06-27T18:07:00-00:00

Ecuador is the third-largest foreign supplier of crude oil to the western United States. As the source of this oil, the Ecuadorian Amazon has borne the far-reaching social and environmental consequences of a growing U.S. demand for petroleum and the dynamics of economic globalization it necessitates._ Crude Chronicles_ traces the emergence during the 1990s of a highly organized indigenous movement and its struggles against a U.S. oil company and Ecuadorian neoliberal policies. Against the backdrop of mounting government attempts to privatize and liberalize the national economy, Suzana Sawyer shows how neoliberal reforms in Ecuador led to a crisis of governance, accountability, and representation that spurred one of twentieth-century Latin America’s strongest indigenous movements. Through her rich ethnography of indigenous marches, demonstrations, occupations, and negotiations, Sawyer tracks the growing sophistication of indigenous politics as Indians subverted, re-deployed, and, at times, capitulated to the dictates and desires of a transnational neoliberal logic. At the same time, she follows the multiple maneuvers and discourses that the multinational corporation and the Ecuadorian state used to circumscribe and contain indigenous opposition. Ultimately, Sawyer reveals that indigenous struggles over land and oil operations in Ecuador were as much about reconfiguring national and transnational inequality—that is, rupturing the silence around racial injustice, exacting spaces of accountability, and rewriting narratives of national belonging—as they were about the material use and extraction of rain-forest resources.

Interactions durables écologie et evolution du parasitisme

Claude Combes — 2007-02-25T14:38:16-00:00

(24 January 2002)

ECOLOGY: Globalization, Roving Bandits, and Marine Resources

F Berkes — 2006-03-18T20:54:26-00:00

Science, Vol. 311, No. 5767. (17 March 2006), pp. 1557-1558.

The worth of a songbird: ecological economics as a post-normal science

Silvio Funtowicz — 2006-09-07T07:48:28-00:00

Ecological Economics, Vol. 10, No. 3. (August 1994), pp. 197-207.

One of the very valuable features of Ecological Economics is its provision for publications under the rubric `Commentary'. In that way, essays which are not research in the strictest sense can still find proper refereed publication, and can be submitted to the further test of open colleague criticism. This paper is intended to be read in that spirit; and where criticisms are made of the work of particular scholars, that is done because of the significance of their contribution.

Introduced species and their missing parasites.

ME Torchin — 2007-02-17T22:39:16-00:00

Nature, Vol. 421, No. 6923. (6 February 2003), pp. 628-630.

Damage caused by introduced species results from the high population densities and large body sizes that they attain in their new location. Escape from the effects of natural enemies is a frequent explanation given for the success of introduced species. Because some parasites can reduce host density and decrease body size, an invader that leaves parasites behind and encounters few new parasites can experience a demographic release and become a pest. To test whether introduced species are less parasitized, we have compared the parasites of exotic species in their native and introduced ranges, using 26 host species of molluscs, crustaceans, fishes, birds, mammals, amphibians and reptiles. Here we report that the number of parasite species found in native populations is twice that found in exotic populations. In addition, introduced populations are less heavily parasitized (in terms of percentage infected) than are native populations. Reduced parasitization of introduced species has several causes, including reduced probability of the introduction of parasites with exotic species (or early extinction after host establishment), absence of other required hosts in the new location, and the host-specific limitations of native parasites adapting to new hosts.

Evolving together: the biology of symbiosis, part 1.

GG Dimijian — 2007-01-03T10:37:13-00:00

Proc (Bayl Univ Med Cent), Vol. 13, No. 3. (July 2000), pp. 217-226.

Symbioses, prolonged associations between organisms often widely separated phylogenetically, are more common in biology than we once thought and have been neglected as a phenomenon worthy of study on its own merits. Extending along a dynamic continuum from antagonistic to cooperative and often involving elements of both antagonism and mutualism, symbioses involve pathogens, commensals, and mutualists interacting in myriad ways over the evolutionary history of the involved "partners." In this first of 2 parts, some remarkable examples of symbiosis will be explored, from the coral-algal symbiosis and nitrogen fixation to the great diversity of dietary specializations enabled by the gastrointestinal microbiota of animals.

Evolving together: the biology of symbiosis, part 2.

GG Dimijian — 2007-01-03T10:36:50-00:00

Proc (Bayl Univ Med Cent), Vol. 13, No. 4. (October 2000), pp. 381-390.

Symbiotic trade-offs dominate the world of biology and medicine in colonist-host relationships and between separate, mutually dependent organisms of different species. Infectious and parasitic diseases can be better understood by exploring the dynamic continuum between pathogenicity and mutualism, between antagonism and cooperation-the sliding scale along which microorganisms can move in a moment's notice with a single nucleotide substitution. Organisms practicing piracy or pastoralism may be close genetic relatives. Mergers occur not only between cells but also between genomes; viruses co-opt host genes and in turn insert themselves into host genomes. Separate organisms, from ants to fungi to plants, establish symbiotic ties with each other that bind over deep time, generating much of the diversity we see in nature.

The Costs of Carnivory

Chris Carbone — 2007-01-22T16:17:04-00:00

PLoS Biology, Vol. 5, No. 2. (1 February 2007), e22.

Mammalian carnivores fall into two broad dietary groups: smaller carnivores (<20 kg) that feed on very small prey (invertebrates and small vertebrates) and larger carnivores (>20 kg) that specialize in feeding on large vertebrates. We develop a model that predicts the mass-related energy budgets and limits of carnivore size within these groups. We show that the transition from small to large prey can be predicted by the maximization of net energy gain; larger carnivores achieve a higher net gain rate by concentrating on large prey. However, because it requires more energy to pursue and subdue large prey, this leads to a 2-fold step increase in energy expenditure, as well as increased intake. Across all species, energy expenditure and intake both follow a three-fourths scaling with body mass. However, when each dietary group is considered individually they both display a shallower scaling. This suggests that carnivores at the upper limits of each group are constrained by intake and adopt energy conserving strategies to counter this. Given predictions of expenditure and estimates of intake, we predict a maximum carnivore mass of approximately a ton, consistent with the largest extinct species. Our approach provides a framework for understanding carnivore energetics, size, and extinction dynamics.

Phylogenies, the comparative method and parasite evolutionary ecology.

S Morand — 2005-10-12T15:49:04-00:00

Adv Parasitol, Vol. 54 (2003), pp. 281-302.

A growing number of comparative analyses in the field of parasite evolution and ecology have used phylogenetically based comparative methods. However, the comparative approach has not been used much by parasitologists. We present the rationale for the use of phylogenetic information in comparative studies, and we illustrate the use of several phylogenetically based comparative methods with case studies in parasite evolutionary ecology. The independent contrasts method is the most popular one, but presents some problems for studying co-adaptation between host and parasite life traits. The eigenvector method has been recently proposed as a new method to estimate and correct for phylogenetic inertia. We illustrate this method with an investigation of patterns of helminth parasite species richness across mammalian host species. This method seems to perform well in situations where host and parasite phylogenies are not perfectly congruent, but one might still want to correct for the effects of both. Finally, we present a method recently proposed for variation partitioning in a phylogenetic context, i.e. the phylogenetically structured environmental variation.

Co-existence of nine gill ectoparasites (Dactylogyrus: monogenea) parasitising the roach (Rutilus rutilus l.): history and present ecology.

A Simková — 2007-01-01T11:29:31-00:00

Int J Parasitol, Vol. 30, No. 10. (September 2000), pp. 1077-1088.

Co-existence among potentially competing species can be favoured by niche specialisation and/or by reducing the overall intensity of competition via aggregated utilisation of fragmented resources. We investigated the respective roles of niche specialisation and aggregation in the case of nine congeneric monogenean parasites on the gills of Roach (Rutilus rutilus L.) belonging to the genus Dactylogyrus. The position of each individual parasite of the nine Dactylogyrus species was recorded. Niche breadth and niche overlap of parasite species were estimated. Comparative methods, which take into account phylogenetic information of the analysed species, were used. We reconstructed a phylogeny of the nine Dactylogyrus species based on morphological characters. We used the 'aggregation model of co-existence' in the model to test if species co-existence is facilitated when intraspecific aggregation exceeds interspecific aggregation. We observed a lack of negative correlation in abundance between pairs of parasites, and a negative correlation between niche size and parasite aggregation, for both intraspecific and interspecific aggregation. Our comparative analysis showed that parasite abundance is positively correlated with niche breadth. Then parasite abundance, and not interactions between Dactylogyrus species, seems to be the most important factor determining niche size This result gives some support to niche segregation by specialisation. Niche size was negatively correlated with both intraspecific and interspecific aggregation. No relationship was found between an increase of interspecific aggregation with an increase of niche overlapping, which suggests that competition may play little role. A lack of competition could be also confirmed by the lack of negative correlation in abundance between species pairs. A parsimony analysis of the evolution of gill distribution indicates a change in one parameter of the niche (arch, segment and/or area) at each branching event.

The impact of parasites on marine mammals: a review.

JA Raga — 2007-03-19T14:55:43-00:00

Parassitologia, Vol. 39, No. 4. (December 1997), pp. 293-296.

The design and implementation of conservation plans for marine mammals is a matter of public concern. However, very little is known about the role of parasites in the dynamics of marine mammal populations. This is probably due to methodological constraints concerning sampling biases, poor knowledge of the biology of the hosts and parasites and difficulty and costy of experimental studies. However, current evidence supports the theory that parasites may regulate marine mammal populations. Crassicauda species in cetaceans and Uncinaria lucasi in pinnipeds seem good candidates as regulating agents. In addition, parasite-induced mass mortalities may be important in marine mammal populations. Well documented cases are the PDV virus which decimated the European common seal (Phoca vitulina) populations in 1988 and the Mediterranean striped dolphin (Stenella coeruleoalba) morbillivirus infection of 1990-1992. Due to the social organisation patterns of marine mammals it is possible that such die-offs occur at very low densities, representing a potential threat to endangered species like the Mediterranean monk seal (Monachus monachus), the Hawaiian monk seal (M. schauinslandi) or the Finish Saimaa seal (Phoca hispida saimensis). It is concluded that parasites can play an important role in marine mammal populations not only at the ecological scale but at the evolutionary one too.

Ecological immunology: costly parasite defences and trade-offs in evolutionary ecology

Ben Sheldon — 2007-01-04T22:44:06-00:00

Trends in Ecology and Evolution, Vol. 11, No. 8. (August 1996), pp. 317-321.

In the face of continuous threats from parasites, hosts have evolved an elaborate series of preventative and controlling measures - the immune system - in order to reduce the fitness costs of parasitism. However, these measures do have associated costs. Viewing an individual's immune response to parasites as being subject to optimization in the face of other demands offers potential insights into mechanisms of life history trade-offs, sexual selection, parasite-mediated selection and population dynamics. We discuss some recent results that have been obtained by practitioners of this approach in natural and semi-natural populations, and suggest some ways in which this field may progress in the near future.

Resolving the paradox of sex and recombination.

SP Otto — 2007-09-27T13:49:56-00:00

Nature Review Genetics, Vol. 3, No. 4. (April 2002), pp. 252-261.

Sexual reproduction and recombination are ubiquitous. However, a large body of theoretical work has shown that these processes should only evolve under a restricted set of conditions. New studies indicate that this discrepancy might result from the fact that previous models have ignored important complexities that face natural populations, such as genetic drift and the spatial structure of populations.

Simple mathematical models with very complicated dynamics.

RM May — 2007-04-02T16:43:48-00:00

Nature, Vol. 261, No. 5560. (10 June 1976), pp. 459-467.

First-order difference equations arise in many contexts in the biological, economic and social sciences. Such equations, even though simple and deterministic, can exhibit a surprising array of dynamical behaviour, from stable points, to a bifurcating hiearchy of stable cycles, to apparently random fluctuations. There are consequently many fascinating problems, some concerned with delicate mathematical aspects of the fine structure of the trajectories, and some concerned with the practical implications and applications. This is an interpretive review of them.

The nature of plant species

Loren Rieseberg — 2006-03-23T02:32:56-00:00

Nature, Vol. 440, No. 7083., pp. 524-527.

Prey-predator system with parental care for predators.

W Wang — 2007-01-14T15:17:58-00:00

J Theor Biol, Vol. 241, No. 3. (7 August 2006), pp. 451-458.

A stage structure is incorporated into a prey-predator model in which predators are split into immature predators and mature predators. It is assumed that immature predators are raised by their parents in the sense that they cannot catch the prey and their foods are provided by parents. Further, it is assumed that the maturation rate of immature predators is a function of the food availability for one immature individual. It is found that the model admits periodic solutions which are produced from the stage structure. Further, it is shown that two stability switches of positive equilibria may occur due to the transition rate incorporating the influence of nutrient, and that the enrichment of adult predators may lead to the catastrophe of the ecological system.

Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence.

R Kalendar — 2007-08-07T09:14:23-00:00

Proc Natl Acad Sci U S A, Vol. 97, No. 12. (6 June 2000), pp. 6603-6607.

The replicative spread of retrotransposons in the genome creates new insertional polymorphisms, increasing retrotransposon numbers and potentially both their share of the genome and genome size. The BARE-1 retrotransposon constitutes a major, dispersed, active component of Hordeum genomes, and BARE-1 number is positively correlated with genome size. We have examined genome size and BARE-1 insertion patterns and number in wild barley, Hordeum spontaneum, in Evolution Canyon, Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates. BARE-1 has been sufficiently active for its insertional pattern to resolve individuals in a way consonant with their ecogeographical distribution in the canyon and to distinguish them from provenances outside the canyon. On both slopes, but especially on the drier south-facing slope, a simultaneous increase in the BARE-1 copy number and a decrease in the relative number lost through recombination, as measured by the abundance of solo long terminal repeats, appear to have driven the BARE-1 share of the genome upward with the height and dryness of the slope. The lower recombinational loss would favor maintenance of more full-length copies, enhancing the ability of the BARE-1 family to contribute to genome size growth. These local data are consistent with regional trends for BARE-1 in H. spontaneum across Israel and therefore may reflect adaptive selection for increasing genome size through retrotransposon activity.

Evolutionary consequences of niche construction and their implications for ecology.

KN Laland — 2007-11-19T08:39:16-00:00

Proc Natl Acad Sci U S A, Vol. 96, No. 18. (31 August 1999), pp. 10242-10247.

Organisms regularly modify local resource distributions, influencing both their ecosystems and the evolution of traits whose fitness depends on such alterable sources of natural selection in environments. We call these processes niche construction. We explore the evolutionary consequences of niche construction using a two-locus population genetic model, which extends earlier analyses by allowing resource distributions to be influenced both by niche construction and by independent processes of renewal and depletion. The analysis confirms that niche construction can be a potent evolutionary agent by generating selection that leads to the fixation of otherwise deleterious alleles, supporting stable polymorphisms where none are expected, eliminating what would otherwise be stable polymorphisms, and generating unusual evolutionary dynamics. Even small amounts of niche construction, or niche construction that only weakly affects resource dynamics, can significantly alter both ecological and evolutionary patterns.

Seasonal and habitat-related distribution pattern of Synechococcus genotypes in Lake Constance

Sven Becker — 2008-02-13T14:40:24-00:00

FEMS Microbiology Ecology, Vol. 62, No. 1. (2007), pp. 64-77.

Abstract The abundance and distribution of Synechococcus spp. in the autotrophic picoplankton of Lake Constance, were followed in the pelagic and littoral habitat by qPCR over 2 years. One genotype, represented by isolated phycoerythrin-rich strain BO 8807, showed a seasonal distribution pattern in both habitats. Before a stable thermal stratification, the maximum of both the Synechococcus population and genotype BO 8807 occurred at 15 or 20 m water depth in the pelagic habitat. During the summer stratification, when the absolute abundance of all Synechococcus spp. was highest above 15 m, the absolute and relative abundance of genotype BO 8807 was maximal at 20 m. These results indicate that Synechococcus spp. or single genotypes are present in deep maxima in Lake Constance. The in situ dynamics of genotype BO 8807 is consistent with the observation that isolated strain BO 8807 requires higher phosphate concentrations for maximum growth rates than a strain from the same phylogenetic cluster that dominates the pelagic summer population. In contrast to these findings, low genome numbers of phycocyanin-rich genotype BO 8805 were found temporarily only in both the littoral and pelagic plankton. Microscopy revealed that PC-rich cells in general occurred preferentially in the littoral habitat. We discuss our results with respect to the versatility of picocyanobacteria of the evolutionary lineage VI of cyanobacteria, and a habitat-related distribution pattern of Synechococcus genotypes.