Pacific Ecoinformatics and Computational Ecology Laboratory

Berkeley, CA, United States

Pacific Ecoinformatics and Computational Ecology Laboratory

Berkeley, CA, United States

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Cohen A.A.,Université de Sherbrooke | Martin L.B.,University of South Florida | Wingfield J.C.,University of California at Davis | McWilliams S.R.,University of Rhode Island | And 2 more authors.
Trends in Ecology and Evolution | Year: 2012

Ecological and evolutionary physiology has traditionally focused on one aspect of physiology at a time. Here, we discuss the implications of considering physiological regulatory networks (PRNs) as integrated wholes, a perspective that reveals novel roles for physiology in organismal ecology and evolution. For example, evolutionary response to changes in resource abundance might be constrained by the role of dietary micronutrients in immune response regulation, given a particular pathogen environment. Because many physiological components impact more than one process, organismal homeostasis is maintained, individual fitness is determined and evolutionary change is constrained (or facilitated) by interactions within PRNs. We discuss how PRN structure and its system-level properties could determine both individual performance and patterns of physiological evolution. © 2012 Elsevier Ltd.


Cleland E.E.,University of California at San Diego | Allen J.M.,University of Connecticut | Crimmins T.M.,United States National Phenology Network | Dunne J.A.,Santa Fe Institute | And 5 more authors.
Ecology | Year: 2012

Earlier spring phenology observed in many plant species in recent decades provides compelling evidence that species are already responding to the rising global temperatures associated with anthropogenic climate change. There is great variability among species, however, in their phenological sensitivity to temperature. Species that do not phenologically "track" climate change may be at a disadvantage if their growth becomes limited by missed interactions with mutualists, or a shorter growing season relative to earlieractive competitors. Here, we set out to test the hypothesis that phenological sensitivity could be used to predict species performance in a warming climate, by synthesizing results across terrestrial warming experiments. We assembled data for 57 species across 24 studies where flowering or vegetative phenology was matched with a measure of species performance. Performance metrics included biomass, percent cover, number of flowers, or individual growth. We found that species that advanced their phenology with warming also increased their performance, whereas those that did not advance tended to decline in performance with warming. This indicates that species that cannot phenologically "track" climate may be at increased risk with future climate change, and it suggests that phenological monitoring may provide an important tool for setting future conservation priorities. © 2012 by the Ecological Society of America.


Thompson R.M.,Monash University | Dunne J.A.,Santa Fe Institute | Dunne J.A.,Pacific Ecoinformatics and Computational Ecology Laboratory | Woodward G.,Queen Mary, University of London
Freshwater Biology | Year: 2012

Food webs are a powerful whole-system way to represent the patterns of biodiversity and energy flow in a readily quantifiable framework amenable to comparative analyses. Integrated theory and data on complex trophic interactions provide useful and novel ways to study ecosystem structure, dynamics, function and stability. Freshwater ecology has contributed considerably to the advancement of food-web ecology. This has occurred through early application of methodological advances such as stable isotope analysis and description of some of the most detailed food webs, including Little Rock Lake and the Broadstone Stream food webs. Freshwater food webs are often highly resolved, although the inclusion of components such as bacteria continues to be challenging. Characteristics of stream food webs appear to include high rates of omnivory and a strong role for body size as a structuring influence. While freshwater ecology has often included landscape factors, food webs from freshwaters have most often been collected at small spatial scales. There is a need to take a landscape approach to the study of food-web dynamics in freshwater ecosystems. Studies of food webs that take an experimental approach or utilise natural gradients remain rare but will be vital to untangling causative relationships between changing environmental conditions and food-web structure and dynamics. Emerging directions in freshwater food-web research involve integrating individual-level variation and information on traits into food-web studies. This is allowing a growing understanding of the ways in which food webs can be used to integrate community, evolutionary and population processes into studies of biodiversity. A Virtual Issue of Freshwater Biology entitled 'Advances in food-web research: a compendium of Freshwater Biology papers' brings together papers included in this review that have been published in the journal since 1985. The Virtual Issue can be located at http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-2427/homepage/virtual_issue_advances_in_food-web_research.htm. © 2012 Blackwell Publishing Ltd.


Thompson R.M.,Monash University | Brose U.,University of Gottingen | Dunne J.A.,Santa Fe Institute | Dunne J.A.,Pacific Ecoinformatics and Computational Ecology Laboratory | And 9 more authors.
Trends in Ecology and Evolution | Year: 2012

The global biodiversity crisis concerns not only unprecedented loss of species within communities, but also related consequences for ecosystem function. Community ecology focuses on patterns of species richness and community composition, whereas ecosystem ecology focuses on fluxes of energy and materials. Food webs provide a quantitative framework to combine these approaches and unify the study of biodiversity and ecosystem function. We summarise the progression of food-web ecology and the challenges in using the food-web approach. We identify five areas of research where these advances can continue, and be applied to global challenges. Finally, we describe what data are needed in the next generation of food-web studies to reconcile the structure and function of biodiversity. © 2012 Elsevier Ltd.


Boit A.,University of Potsdam | Martinez N.D.,Pacific Ecoinformatics and Computational Ecology Laboratory | Williams R.J.,Microsoft | Williams R.J.,Quid Inc | Gaedke U.,University of Potsdam
Ecology Letters | Year: 2012

Mechanistic understanding of consumer-resource dynamics is critical to predicting the effects of global change on ecosystem structure, function and services. Such understanding is severely limited by mechanistic models' inability to reproduce the dynamics of multiple populations interacting in the field. We surpass this limitation here by extending general consumer-resource network theory to the complex dynamics of a specific ecosystem comprised by the seasonal biomass and production patterns in a pelagic food web of a large, well-studied lake. We parameterised our allometric trophic network model of 24 guilds and 107 feeding relationships using the lake's food web structure, initial spring biomasses and body-masses. Adding activity respiration, the detrital loop, minimal abiotic forcing, prey resistance and several empirically observed rates substantially increased the model's fit to the observed seasonal dynamics and the size-abundance distribution. This process illuminates a promising approach towards improving food-web theory and dynamic models of specific habitats. © 2012 Blackwell Publishing Ltd/CNRS.


Lafferty K.D.,U.S. Geological Survey | Dunne J.A.,Santa Fe Institute | Dunne J.A.,Pacific Ecoinformatics and Computational Ecology Laboratory
Theoretical Ecology | Year: 2010

Stochastic ecological network occupancy (SENO) models predict the probability that species will occur in a sample of an ecological network. In this review, we introduce SENO models as a means to fill a gap in the theoretical toolkit of ecologists. As input, SENO models use a topological interaction network and rates of colonization and extinction (including consumer effects) for each species. A SENO model then simulates the ecological network over time, resulting in a series of sub-networks that can be used to identify commonly encountered community modules. The proportion of time a species is present in a patch gives its expected probability of occurrence, whose sum across species gives expected species richness. To illustrate their utility, we provide simple examples of how SENO models can be used to investigate how topological complexity, species interactions, species traits, and spatial scale affect communities in space and time. They can categorize species as biodiversity facilitators, contributors, or inhibitors, making this approach promising for ecosystem-based management of invasive, threatened, or exploited species. © 2010 The Author(s).


Brose U.,University of Gottingen | Dunne J.A.,Santa Fe Institute | Dunne J.A.,Pacific Ecoinformatics and Computational Ecology Laboratory | Montoya J.M.,CSIC - Institute of Marine Sciences | And 3 more authors.
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2012

One important aspect of climate change is the increase in average temperature, which will not only have direct physiological effects on all species but also indirectly modifies abundances, interaction strengths, food-web topologies, community stability and functioning. In this theme issue, we highlight a novel pathway through which warming indirectly affects ecological communities: by changing their size structure (i.e. the body-size distributions). Warming can shift these distributions towards dominance of small- over large-bodied species. The conceptual, theoretical and empirical research described in this issue, in sum, suggests that effects of temperature may be dominated by changes in size structure, with relatively weak direct effects. For example, temperature effects via size structure have implications for top-down and bottom-up control in ecosystems and may ultimately yield novel communities. Moreover, scaling up effects of temperature and body size from physiology to the levels of populations, communities and ecosystems may provide a crucially important mechanistic approach for forecasting future consequences of global warming. © 2012 The Royal Society.


Srinivasan U.T.,Pacific Ecoinformatics and Computational Ecology Laboratory
Climate Policy | Year: 2010

The impacts of predicted climate change will not be distributed evenly around the world. As post-Kyoto negotiations unfold, relating the geographical distribution of projected impacts to responsibility for emissions among world regions is essential for achieving an equitable path forward. This article surveys the current knowledge of regional climate consequences, and delves into the regional predictions of economic assessment models to date, examining how the uncertainties, assumptions and ethical dimensions influence the portrayal of risk at this scale. The few studies that quantitatively compared regional risk and responsibility are reviewed, and the analytical framework from one such study is applied to the 2006 Stern Review's projections to give the first regional comparison to take purchasing power and welfare considerations into account. Synthesizing burden and blame in this way is informative for policy makers; the world's most vulnerable communities - in Africa, the Indian subcontinent, Latin America, and small island states - accounted for less than 33% of global greenhouse gas emissions over the period 1961-2000, but may experience more than 75% of the ensuing climate damages this century. This analysis reinforces the call for industrialized nations to lead mitigation efforts, and to do so decisively and swiftly. © 2010 Earthscan.


Srinivasan U.T.,Pacific Ecoinformatics and Computational Ecology Laboratory | Srinivasan U.T.,University of British Columbia | Watson R.,University of British Columbia | Rashid Sumaila U.,University of British Columbia
Marine Policy | Year: 2012

Up to one-third of commercial fishery stocks may be overfished at present. By analyzing catch trends and applying an empirical relationship derived from stock assessments, this article tracks the geographic spread of overfishing at the country level in terms of lost catch and lost revenue, from the start of industrialized fishing in 1950-2004. The results tell a cautionary tale of serial depletion to meet the ever-rising demand for fish. Examining country losses with respect to fishery management reveals that overcapacity and excess fishing effort are widespread, but also that recent trends towards sustainability can stabilize or reverse losses (e.g. for Norway, Iceland, the US, Canada, Australia, and New Zealand). Global trade effectively masks the successive depletion of stocks, so that without decisive action to reduce fishing effort, many more stocks will suffer and undernourishment impacts for the major exporting, food-deficit nations will only magnify. © 2011 Elsevier Ltd.


Lotze H.K.,Dalhousie University | Coll M.,Dalhousie University | Coll M.,CSIC - Institute of Marine Sciences | Dunne J.A.,Santa Fe Institute | Dunne J.A.,Pacific Ecoinformatics and Computational Ecology Laboratory
Ecosystems | Year: 2011

The Mediterranean Sea has been strongly influenced by human activities for millennia. Although the environmental history of its surrounding terrestrial ecosystems has received considerable study, historical changes in its marine realm are less known. We used a multidisciplinary approach combining paleontological, archeological, historical, fisheries, and ecological data to reconstruct past changes in marine populations, habitats, and water quality in the Adriatic Sea. Then, we constructed binary food webs for different historical periods to analyze possible changes in food-web structure and functioning over time. Our results indicate that human activities have influenced marine resource abundance since at least Roman times and accelerated in the nineteenth and twentieth centuries. Today, 98% of traditional marine resources are depleted to less than 50% of former abundance, with large (>1 m) predators and consumers being most affected. With 37% of investigated species rare and 11% extirpated, diversity has shifted towards smaller, lower trophic-level species, further aggravated by more than 40 species invasions. Species providing habitat and filter functions have been reduced by 75%, contributing to the degradation of water quality and increased eutrophication. Increased exploitation and functional extinctions have altered and simplified food-web structure over time, especially by changing the proportions of top predators, intermediate consumers, and basal species. Moreover, simulations of species losses indicate that today's ecosystems may be less robust to species extinctions than in the past. Our results illustrate the long-term and far-reaching consequences human activities can have on marine food webs and ecosystems. © 2010 Springer Science+Business Media, LLC.

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