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Analysis of Biological Networks Network Analysis Analysis of Biological Networks Network Analysis Ecological Networks Spring 2020 Sharif University of Technology Ecological Networks Part I: Basic Concepts Part I: Basic Concepts • Ecology: is the study of the relationships between living organisms, including humans, and their physical environment; it seeks to understand the vital connections between plants and animals and the world around them. • Ecosystem: is a community of living organisms in conjunction with the nonliving components of their environment, interacting as a system. Part I: Basic Concepts • Biological interaction (Biotic interaction): is the effect that a pair of organisms living together in a community have on each other. • Symbiosis: is any type of a close and long-term biological interaction between two different biological organisms, that can be mutualistic, commensalistic, or parasitic. • Mutualism: describes the ecological interaction between two or more species where each species has a net benefit. • Ecological Stability: An ecosystem is said to possess ecological stability (or equilibrium) if it is capable of returning to its equilibrium state after a perturbation (resilience) or does not experience unexpected large changes in its characteristics across time. Ecological Network (EN) Part II: What is EN? Part II: What is EN? • Food web (or food cycle or trophic): is the natural interconnection of food chains as a graphical representation of what-eats-what in an ecological community. Part II: What is EN • Ecological network: is a representation of the biotic interactions in an ecosystem, in which species (nodes) are connected by pairwise interactions (links). • These interactions can be trophic or symbiotic. • Ecological networks are used to describe and compare the structures of real ecosystems, while network models are used to investigate the effects of network structure on properties such as ecosystem stability. Ecological Network (EN) Part III: Ecological Network Properties Part III: EN Properties? • Research in ecological networks developed from descriptions of trophic relationships in food webs. • However, recent work has expanded to look at other food webs as well as webs of mutualists as complex networks with certain properties. • Complexity (linkage density): the average number of links per species. Explaining the observed high levels of complexity in ecosystems has been one of the main challenges and motivations for ecological network analysis, since early theory predicted that complexity should lead to instability. Part III: EN Properties? • Connectivity: the proportion of possible links between species that are realized (links/species2). In food webs, the level of connectivity is related to the statistical distribution of the links per species. • The distribution of links changes from (partial) power-law to exponential to uniform as the level of connectivity increases. • The observed values of connectivity in empirical food webs appear to be accountable for by constraints on an organisms diet breadth. • This links the structure of these ecological networks to the behavior of individual organisms. Part III: EN Properties? • Degree distribution: the degree distribution of an ecological network is the cumulative distribution for the number of links each species has. • The degree distributions of food webs have been found to display the same universal functional form. • The degree distribution can be split into its two component parts, links to a species' prey (in degree) and links to a species' predators (out degree). • As there is a faster decay of the out-degree distribution than the in degree distribution we can expect that on average in a food web a species will have more in links than out links. Part III: EN Properties? • Clustering: the proportion of species that are directly linked to a focal species. A focal species in the middle of a cluster may be a keystone species, and its loss could have large effects on the network. • Compartmentalization: the division of the network into relatively independent sub-networks. Some ecological networks have been observed to be compartmentalized by body size and by spatial location. • Evidence also exists which suggests that compartmentilization in food webs appears to result from patterns of species' diet contiguity and adaptive foraging. Part III: EN Properties? • Nestedness: the degree to which species with few links have a sub-set of the links of other species, rather than a different set of links. • In highly nested networks, guilds of species that share an ecological niche contain both generalists (species with many links) and specialists (species with few links, all shared with the generalists). • Nestedness is often asymmetrical, with specialists of one guild linked to the generalists of the partner guild. • The level of nestedness is determined not by species features but overall network depictors (e.g. network size and connectivity). Part III: EN Properties? • Network Motif: Motifs are unique sub-graphs composed of n-nodes found embedded in a network. • For example if there exist thirteen unique motif structures containing three species, some of these correspond to familiar interaction modules studied by population ecologists such as food chains, apparent competition, or intraguild predation. • Studies investigating motif structures of ecological networks, by examining patterns of under/over representation of certain motifs compared to a random graph, have found that food webs have particular motif structures. Part III: EN Properties? • Trophic coherence: The tendency of species to specialize on particular trophic levels leads to food webs displaying a significant degree of order in their trophic structure, known as trophic coherence, which in turn has important effects on properties such as stability. • Introduction to Ecological Networks. Ecological Networks Part IV: Case Study: Network Analysis 16 Summary • Finding dataset • Data description • Analyzing network • Conclusion Cytoscape • We use Cytoscape for ecological network analysis Finding dataset • We can find dataset from different database – ECOLOGY NETWORKS • http://networkrepository.com/eco.php – foodwebs: A collection of food webs • https://rdrr.io/cran/igraphdata/man/foodwebs.html – …. Data description • Food web from Maspalomas lagoon – Study location • The ‘ Charca de Maspalomas ’a small, shallow subtropical coastal lagoon, located on the southern coast of Gran Canaria (Canary Islands). – It is directed weighed graph: • Nodes : the species – The ’Biomass’ node attribute contains the biomass of the species. • Edges : energy flux between the species involved Data description (cont.) • A GraphML file consists of an XML file containing a graph element Analyzing the network • We want to Analyze the properties of the food web • Open file : – File à import à network from file … à select Maspalomas.graphml • Analyze: – Tools à Analyze network • Now we can Calculate some properties of food webs : – Complexity – Node degree – Maximum chain length – …. Visualization of the network Visualization of the network (cont.) • To see the direction of flows you can change the Arrow shape from: left menu à style à Edge tab à source arrow shape Energy flux • We can select each edge and see the weight of each energy flux between two species Respiration • We can see the respiration of each node by clicking on the edge between that and the Repression node • You can also see DOC and POC flows. Complexity • Complexity has been one of the main challenges and motivations for ecological network analysis since early theory predicted that complexity should lead to instability. complexity is often expressed by the size and connectance (density) of the web. degree distribution of the nodes show that although (2002ـThe results of (Dunne • some food webs have small-world and scale-free structure, most do not if they exceed a relatively low level of connectance. Maximum chain length show that the (2002ـThe results of (Kondoh • maximum chain length decreases with resource availability in some food webs. Conclusion • We can compute food web properties by cytoscape – Complexity – Node degree – Maximum chain length – …. • So we can compare different food webs by these metrics – Food webs in different locations – Food webs in different seasons Refrences • [1] Dunne, Jennifer A., Richard J. Williams, and Neo D. Martinez. "Food-web structure and network theory: the role of connectance and size." Proceedings of the National Academy of Sciences 99.20 (2002): 12917-12922. • [2] Kondoh, Michio, and Kunihiko Ninomiya. "Food-chain length and adaptive foraging." Proceedings of the Royal Society B: Biological Sciences 276.1670 (2009): 3113-3121. Ecological Network Part V: Summary & Conclusions Summary of Ecological Networks • Ecological networks typically represent food webs that may be defined as networks of consumer–resource interactions between groups of organisms. • In food webs, the vertices (nodes, points) are represented by individual species, certain life stages of one species, or by an aggregation of species (trophic guild). • Ecological networks facilitate a comprehensive understanding and forecasting of the dynamics of ecosystems..
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