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Using food web dominator trees to catch secondary extinctions in action.

ABSTRACT: In ecosystems, a single extinction event can give rise to multiple 'secondary' extinctions. Conservation effort would benefit from tools that help forecast the consequences of species removal. One such tool is the dominator tree, a graph-theoretic algorithm that when applied to food webs unfolds their complex architecture, yielding a simpler topology made of linear pathways that are essential for energy delivery. Each species along these chains is responsible for passing energy to the taxa that follow it and, as such, it is indispensable for their survival. To assess the predictive potential of the dominator tree, we compare its predictions with the effects that followed the collapse of the capelin (Mallotus villosus) in the Barents Sea ecosystem. To this end, we first compiled a food web for this ecosystem, then we built the corresponding dominator tree and, finally, we observed whether model predictions matched the empirical observations. This analysis shows the potential and the drawbacks of the dominator trees as a tool for understanding the causes and consequences of extinctions in food webs.

SUBMITTER: Bodini A

PROVIDER: S-EPMC2685427 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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Using food web dominator trees to catch secondary extinctions in action.

Bodini Antonio A Bellingeri Michele M Allesina Stefano S Bondavalli Cristina C

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 20090601 1524

In ecosystems, a single extinction event can give rise to multiple 'secondary' extinctions. Conservation effort would benefit from tools that help forecast the consequences of species removal. One such tool is the dominator tree, a graph-theoretic algorithm that when applied to food webs unfolds their complex architecture, yielding a simpler topology made of linear pathways that are essential for energy delivery. Each species along these chains is responsible for passing energy to the taxa that ...[more]

PMID: 19451123

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Project description:We measured food availability and diet composition of juvenile salmonids over multiple years and seasons before and during the world's largest dam removal on the Elwha River, Washington State. We conducted these measurements over three sediment-impacted sections (the estuary and two sections of the river downstream of each dam) and compared these to data collected from mainstem tributaries not directly affected by the massive amount of sediment released from the reservoirs. We found that sediment impacts from dam removal significantly reduced invertebrate prey availability, but juvenile salmon adjusted their foraging so that the amount of energy in diets was similar before and during dam removal. This general pattern was seen in both river and estuary habitats, although the mechanisms driving the change and the response differed between habitats. In the estuary, the dietary shifts were related to changes in invertebrate assemblages following a hydrological transition from brackish to freshwater caused by sediment deposition at the river's mouth. The loss of brackish invertebrate species caused fish to increase piscivory and rely on new prey sources such as plankton. In the river, energy provided to fish by Ephemeroptera, Plecoptera, and Trichoptera taxa before dam removal was replaced first by terrestrial invertebrates, and then by sediment-tolerant taxa such as Chironomidae. The results of our study are consistent with many others that have shown sharp declines in invertebrate density during dam removal. Our study further shows how those changes can move through the food web and affect fish diet composition, selectivity, and energy availability. As we move further along the dam removal response trajectory, we hypothesize that food web complexity will continue to increase as annual sediment load now approaches natural background levels, anadromous fish have recolonized the majority of the watershed between and above the former dams, and revegetation and microhabitats continue to develop in the estuary.

Project description:BackgroundIt has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure.ResultsThe statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure.ConclusionSearch algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These preliminary findings demonstrate that graph-theoretic quantifiers utilized in fields such as computer network design hold significant promise as an added tool for genomics and proteomics.

Dataset Information

Using food web dominator trees to catch secondary extinctions in action.

Publications

Using food web dominator trees to catch secondary extinctions in action.

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