Significant Scales in Community Structure

Many complex networks show signs of modular structure, uncovered by community detection. Although many methods succeed in revealing various partitions, it remains difficult to detect at what scale some partition is significant. This problem shows foremost in multi-resolution methods. We here introduce an efficient method for scanning for resolutions in one such method. Additionally, we introduce the notion of "significance" of a partition, based on subgraph probabilities. Significance is independent of the exact method used, so could also be applied in other methods, and can be interpreted as the gain in encoding a graph by making use of a partition. Using significance, we can determine "good" resolution parameters, which we demonstrate on benchmark networks. Moreover, optimizing significance itself also shows excellent performance. We demonstrate our method on voting data from the European Parliament. Our analysis suggests the European Parliament has become increasingly ideologically divided and that nationality plays no role.Comment: To appear in Scientific Report

A shadowing problem in the detection of overlapping communities: lifting the resolution limit through a cascading procedure

Community detection is the process of assigning nodes and links in significant communities (e.g. clusters, function modules) and its development has led to a better understanding of complex networks. When applied to sizable networks, we argue that most detection algorithms correctly identify prominent communities, but fail to do so across multiple scales. As a result, a significant fraction of the network is left uncharted. We show that this problem stems from larger or denser communities overshadowing smaller or sparser ones, and that this effect accounts for most of the undetected communities and unassigned links. We propose a generic cascading approach to community detection that circumvents the problem. Using real and artificial network datasets with three widely used community detection algorithms, we show how a simple cascading procedure allows for the detection of the missing communities. This work highlights a new detection limit of community structure, and we hope that our approach can inspire better community detection algorithms.Comment: 14 pages, 12 figures + supporting information (5 pages, 6 tables, 3 figures

The anatomy of urban social networks and its implications in the searchability problem

The appearance of large geolocated communication datasets has recently increased our understanding of how social networks relate to their physical space. However, many recurrently reported properties, such as the spatial clustering of network communities, have not yet been systematically tested at different scales. In this work we analyze the social network structure of over 25 million phone users from three countries at three different scales: country, provinces and cities. We consistently find that this last urban scenario presents significant differences to common knowledge about social networks. First, the emergence of a giant component in the network seems to be controlled by whether or not the network spans over the entire urban border, almost independently of the population or geographic extension of the city. Second, urban communities are much less geographically clustered than expected. These two findings shed new light on the widely-studied searchability in self-organized networks. By exhaustive simulation of decentralized search strategies we conclude that urban networks are searchable not through geographical proximity as their country-wide counterparts, but through an homophily-driven community structure

Examining neotropical primate community structure at regional and local scales : insights from taxonomic and phylogenetic approaches

Understanding mechanisms underlying distribution of biodiversity remains a central issue in ecology. I integrate ecological and phylogenetic information at multiple spatial scales to better understand neotropical primate distribution and community structure. I investigate the variation within species ranges in relation to species richness and patterns of species relatedness. Results suggest positive associations among species throughout their distributions, whereby species tend to present higher richness within their ranges than average richness for the entire taxon. However, comparing empirical distributions to a null model of range cohesion suggests mechanisms other than dispersal are setting a limit to the number of species capable of co-occurring throughout a species’ range. These differences in species associations across geographic ranges generate variation in local community composition. I analyzed the relative contribution of ecological, historical and spatial processes in determining taxonomic and phylogenetic community structure across 74 sites throughout the Neotropics. Spatial predictors explained most of the independent variation for taxonomic and phylogenetic metrics, suggesting spatial processes, such as dispersal limitation, are important determinants of community structure. Most of the contribution of environmental predictors was associated with spatial processes, evincing importance of environmental and spatial gradients in determining change in community structure. While the overall contributions of predictors were similar for taxonomic and phylogenetic metrics, analyses of phylogenetic metrics independently presented complex relationships. At local communities, niche differentiation is expected to allow species coexistence. However, these differences may reflect evolutionary constraints of species, rather than active selection. I investigated niche overlap and presence of niche conservatism for primate species at three communities. For the niche characteristics measured by my study, I found no significant differences in niches of closely related species within sites. However, when comparing niches across sites, significant differences were registered between populations of the same species or closely related species. These findings suggest ecological differentiation may be acting at large spatial scales promoting niche differentiation, while at local scales phylogenetic constraints may be a stronger driver of community structure. Overall, these results represent valuable insights regarding our understanding of mechanisms responsible for generating and maintaining community structure for a highly diverse tropical mammal radiation

Peat properties, dominant vegetation type and microbial community structure in a tropical peatland

Tropical peatlands are an important carbon store and source of greenhouse gases, but the microbial component, particularly community structure, remains poorly understood. While microbial communities vary between tropical peatland land uses, and with biogeochemical gradients, it is unclear if their structure varies at smaller spatial scales as has been established for a variety of peat properties. We assessed the abundances of PLFAs and GDGTs, two membrane spanning lipid biomarkers in bacteria and fungi, and bacteria and archaea, respectively, to characterise peat microbial communities under two dominant and contrasting plant species, Campnosperma panamensis (a broadleaved evergreen tree), and Raphia taedigera (a canopy palm), in a Panamanian tropical peatland. The plant communities supported similar microbial communities dominated by Gram negative bacteria (38.9–39.8%), with smaller but significant fungal and archaeal communities. The abundance of specific microbial groups, as well as the ratio of caldarchaeol:crenarchaeol, isoGDGT: brGDGTs and fungi:bacteria were linearly related to gravimetric moisture content, redox potential, pH and organic matter content indicating their role in regulating microbial community structure. These results suggest that tropical peatlands can exhibit significant variability in microbial community abundance even at small spatial scales, driven by both peat botanical origin and localised differences in specific peat properties

The Role of Fine-Scale Habitat Associations in Structuring Spider Assemblages: Determinants of Spatial Patterns in Community Composition

Elucidating the ecological determinants of community structure and how they vary spatially has a long history in ecology, but there still is no consensus on the mechanisms behind diversity patterns. The primary objective of this dissertation was to focus on spider assemblages to investigate how the fine-scale habitat associations of organisms may drive their community composition at larger scales. Research was conducted in the Bear River Mountains, Utah, in an attempt to elucidate the potential role of species-microhabitat associations in driving three well-known patterns of community composition that have typically been investigated at broad scales: 1) elevation gradients of species diversity, 2) the response of species assemblages to neighboring habitat structure and 3) community composition at the edges of habitat patches. Slope aspect was a significant predictor of spider density and species richness when communities were compared at the same elevation, suggesting that fine-scale topographic variables may play an important role in shaping elevational patterns of species composition. Cursorial spider composition was strongly linked to site temperature only, whereas differences across web spider assemblages significantly increased with dissimilarities in woody plant cover and temperature. The study on the effects of neighboring habitat structure revealed markedly reduced cursorial spider densities in shrubs without surrounding structure, and more cursorial species in control shrubs, whereas web spiders lacked any significant response to treatments. These contrasting responses indicate that data should be collected at larger spatial extents for mobile species, and that mobility may mediate the outcome of surrounding habitat modifications on the local composition of communities. In the last study, I focused on communities in which the edge-dwelling spiders Theridion and Dictyna strongly differed in terms of concealment and substrate generalization and found that microhabitat choice may affect the sensitivity of species to habitat geometry, a characteristic associated with habitat fragmentation. This work suggests that a better understanding of the links between the biological traits of species and their fine-scale environmental requirements may help uncover the mechanisms behind spatial patterns of community composition at larger scales

Spatial characterization of arbuscular mycorrhizal fungal molecular diversity at the submetre scale in a temperate grassland

Although arbuscular mycorrhizal fungi (AMF) form spatially complex communities in terrestrial ecosystems, the scales at which this diversity manifests itself is poorly understood. This information is critical to the understanding of the role of AMF in plant community composition. We examined small-scale (submetre) variability of AMF community composition (terminal restriction fragment length polymorphism fingerprinting) and abundance (extraradical hyphal lengths) in two 1 m2 plots situated in a native grassland ecosystem of western Montana. Extraradical AMF hyphal lengths varied greatly between samples (14–89 m g soil−1) and exhibited spatial structure at scales <30 cm. The composition of AMF communities was also found to exhibit significant spatial autocorrelation, with correlogram analyses suggesting patchiness at scales <50 cm. Supportive of overall AMF community composition analyses, individual AMF ribotypes corresponding to specific phylogenetic groups exhibited distinct spatial autocorrelation. Our results demonstrate that AMF diversity and abundance can be spatially structured at scales of <1 m. Such small-scale heterogeneity in the soil suggests that establishing seedlings may be exposed to very different, location dependent AMF communities. Our results also have direct implications for representative sampling of AMF communities in the field