Search arXivSearch

arXiv · 1403.2352

Trophic groups and modules: two levels of group detection in food webs

Abstract

Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups, which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group definitions remains unknown in empirical food webs because they have so far been studied separately. While recent developments in network theory have led to efficient methods for detecting modules in food webs, the determination of trophic groups (sets of species that are functionally similar) is based on subjective expert knowledge. Here, we develop a novel algorithm for trophic group detection. We apply this method to several well-resolved empirical food webs, and show that aggregation into trophic groups allows the simplification of food webs while preserving their information content. Furthermore, we reveal a 2-level hierarchical structure where modules partition food webs into large bottom-top trophic pathways whereas trophic groups further partition these pathways into sets of species with similar trophic connections. Bringing together trophic groups and modules provides new perspectives to the study of dynamical and functional consequences of food-web structure, bridging topological analysis and dynamical systems. Trophic groups have a clear ecological meaning in terms of trophic similarity, and are found to provide a trade-off between network complexity and information loss.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Benoit Gauzens, Elisa Thébault, Gérard Lacroix, Stéphane Legendre. 2015-04-13. Trophic groups and modules: two levels of group detection in food webs. https://arxiv.org/abs/1403.2352

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

Evolution as fitness landscape navigation: concepts, measures, and emerging questions

Fitness landscapes are mappings between genotypes, phenotypes, and fitness that shape evolution. In recent years, empirical work and theoretical models have greatly advanced our understanding of how populations navigate rugged fitness landscapes. Here, we provide a timely review of the theoretical aspects of this field. Its rapidly growing literature employs a wide range of terms, which are sometimes used ambiguously or inconsistently. We therefore begin by defining the major concepts and the field's vocabulary, highlighting our own terminology choices wherever needed. We then review key results on the relationships between epistasis, ruggedness, accessibility, and navigability for genotype-fitness maps, highlighting several complex and sometimes counterintuitive connections that have emerged. Further, we review how the conserved structural properties of the underlying genotype-phenotype map, which can lead to the formation of large connected neutral networks of genotypes, influence dynamics on fitness landscapes. We then compare the two levels to study landscape navigation: the level of genotype-phenotype maps and the level of genotype-fitness maps. Our review leads us to propose a new measure of navigability, based on evolutionary outcomes, that is broadly applicable and overcomes limitations of existing measures. Finally, we highlight examples from the smaller body of work that relaxes the common assumption of fitness-monotonic paths on static landscapes, and discuss how this can fundamentally change the nature of fitness landscape navigation. Throughout the review, we identify directions for future work to fill existing gaps and to synthesize the disparate strands of research within the field.

q-bio.PE

Best Matches in Phylogenetic Networks

Best match graphs (BMGs) were introduced in mathematical phylogenetics to describe the concept of closest relatives for related genes (leaves of rooted tree) in different organisms (defining leaf colors). We generalize this concept here to leaf-colored rooted networks, where least common ancestors are in general neither unique nor comparable. We characterize BMGs of rooted networks as those vertex-colored digraphs that are properly colored and satisfy an easy-to-check condition that we call the sicor-in-hub property. BMGs can be recognized in linear time and an explaining network can be constructed in quadratic time. Analogous results are obtained for reciprocal best match graphs (RBMGs), where an edge $\{x,y\}$ corresponds to pairs of vertices with different color that are mutually closest relatives.

q-bio.PE

Exact Counts of Binary Phylogenetic Networks with Four Reticulations

Phylogenetic networks provide a flexible framework for representing reticulate evolutionary processes, such as hybridization, introgression, recombination, and horizontal gene transfer. However, their combinatorial complexity makes even basic enumeration problems difficult. Building on our previous work for networks with up to three reticulations, we derive an explicit closed-form formula for the number of unrestricted rooted binary phylogenetic networks with four reticulations on \(n\) labeled taxa. Our approach is based on tree-component graphs. We classify the 79 possible component graphs corresponding to networks with four reticulations into ten groups. We then enumerate the networks associated with each group by combining known counts of one-component networks, forests, and networks with fewer reticulations. Summing these contributions yields the desired formula. This result extends the exact enumeration of unrestricted binary phylogenetic networks to four reticulations and further demonstrates the effectiveness of component graphs for systematically organizing and counting increasingly complex network classes.

q-bio.PE