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Concept: Networks


Social networks show striking structural regularities, and both theory and evidence suggest that networks may have facilitated the development of large-scale cooperation in humans. Here, we characterize the social networks of the Hadza, a population of hunter-gatherers in Tanzania. We show that Hadza networks have important properties also seen in modernized social networks, including a skewed degree distribution, degree assortativity, transitivity, reciprocity, geographic decay and homophily. We demonstrate that Hadza camps exhibit high between-group and low within-group variation in public goods game donations. Network ties are also more likely between people who give the same amount, and the similarity in cooperative behaviour extends up to two degrees of separation. Social distance appears to be as important as genetic relatedness and physical proximity in explaining assortativity in cooperation. Our results suggest that certain elements of social network structure may have been present at an early point in human history. Also, early humans may have formed ties with both kin and non-kin, based in part on their tendency to cooperate. Social networks may thus have contributed to the emergence of cooperation.

Concepts: Sociology, Networks, Social psychology, Social network, Human evolution, Network theory, Complex network, Six degrees of separation


Superpositions of social networks, such as communication, friendship, or trade networks, are called multiplex networks, forming the structural backbone of human societies. Novel datasets now allow quantification and exploration of multiplex networks. Here we study gender-specific differences of a multiplex network from a complete behavioral dataset of an online-game society of about 300,000 players. On the individual level females perform better economically and are less risk-taking than males. Males reciprocate friendship requests from females faster than vice versa and hesitate to reciprocate hostile actions of females. On the network level females have more communication partners, who are less connected than partners of males. We find a strong homophily effect for females and higher clustering coefficients of females in trade and attack networks. Cooperative links between males are under-represented, reflecting competition for resources among males. These results confirm quantitatively that females and males manage their social networks in substantially different ways.

Concepts: Human, Male, Female, Sociology, Networks, Society, Social network, Network theory


Intergroup violence is common among humans worldwide. To assess how within-group social dynamics contribute to risky, between-group conflict, we conducted a 3-y longitudinal study of the formation of raiding parties among the Nyangatom, a group of East African nomadic pastoralists currently engaged in small-scale warfare. We also mapped the social network structure of potential male raiders. Here, we show that the initiation of raids depends on the presence of specific leaders who tend to participate in many raids, to have more friends, and to occupy more central positions in the network. However, despite the different structural position of raid leaders, raid participants are recruited from the whole population, not just from the direct friends of leaders. An individual’s decision to participate in a raid is strongly associated with the individual’s social network position in relation to other participants. Moreover, nonleaders have a larger total impact on raid participation than leaders, despite leaders' greater connectivity. Thus, we find that leaders matter more for raid initiation than participant mobilization. Social networks may play a role in supporting risky collective action, amplify the emergence of raiding parties, and hence facilitate intergroup violence in small-scale societies.

Concepts: Participation, E-participation, Sociology, Networks, Social network, Network theory, Standard RAID levels


Human communication in social networks is dominated by emergent statistical laws such as non-trivial correlations and temporal clustering. Recently, we found long-term correlations in the user’s activity in social communities. Here, we extend this work to study the collective behavior of the whole community with the goal of understanding the origin of clustering and long-term persistence. At the individual level, we find that the correlations in activity are a byproduct of the clustering expressed in the power-law distribution of inter-event times of single users, i.e. short periods of many events are separated by long periods of no events. On the contrary, the activity of the whole community presents long-term correlations that are a true emergent property of the system, i.e. they are not related to the distribution of inter-event times. This result suggests the existence of collective behavior, possibly arising from nontrivial communication patterns through the embedding social network.

Concepts: Time, Sociology, Networks, Community, Social network, Network theory, Network science, Complex network


Reconstructing gene regulatory networks (GRNs) from expression data is one of the most important challenges in systems biology research. Many computational models and methods have been proposed to automate the process of network reconstruction. Inferring robust networks with desired behaviours remains challenging, however. This problem is related to network dynamics but has yet to be investigated using network modeling.

Concepts: DNA, Gene, Genetics, Gene expression, Evolution, Organism, Gene regulatory network, Networks


Understanding the complex regulatory networks underlying development and evolution of multi-cellular organisms is a major problem in biology. Computational models can be used as tools to extract the regulatory structure and dynamics of such networks from gene expression data. This approach is called reverse engineering. It has been successfully applied to many gene networks in various biological systems. However, to reconstitute the structure and non-linear dynamics of a developmental gene network in its spatial context remains a considerable challenge. Here, we address this challenge using a case study: the gap gene network involved in segment determination during early development of Drosophila melanogaster. A major problem for reverse-engineering pattern-forming networks is the significant amount of time and effort required to acquire and quantify spatial gene expression data. We have developed a simplified data processing pipeline that considerably increases the throughput of the method, but results in data of reduced accuracy compared to those previously used for gap gene network inference. We demonstrate that we can infer the correct network structure using our reduced data set, and investigate minimal data requirements for successful reverse engineering. Our results show that timing and position of expression domain boundaries are the crucial features for determining regulatory network structure from data, while it is less important to precisely measure expression levels. Based on this, we define minimal data requirements for gap gene network inference. Our results demonstrate the feasibility of reverse-engineering with much reduced experimental effort. This enables more widespread use of the method in different developmental contexts and organisms. Such systematic application of data-driven models to real-world networks has enormous potential. Only the quantitative investigation of a large number of developmental gene regulatory networks will allow us to discover whether there are rules or regularities governing development and evolution of complex multi-cellular organisms.

Concepts: Gene, Genetics, Gene expression, Developmental biology, Cellular differentiation, Gene regulatory network, Networks, Systems biology


We introduce a new method for detecting communities of arbitrary size in an undirected weighted network. Our approach is based on tracing the path of closest-friendship between nodes in the network using the recently proposed Generalized Erds Numbers. This method does not require the choice of any arbitrary parameters or null models, and does not suffer from a system-size resolution limit. Our closest-friend community detection is able to accurately reconstruct the true network structure for a large number of real world and artificial benchmarks, and can be adapted to study the multi-level structure of hierarchical communities as well. We also use the closeness between nodes to develop a degree of robustness for each node, which can assess how robustly that node is assigned to its community. To test the efficacy of these methods, we deploy them on a variety of well known benchmarks, a hierarchal structured artificial benchmark with a known community and robustness structure, as well as real-world networks of coauthorships between the faculty at a major university and the network of citations of articles published in Physical Review. In all cases, microcommunities, hierarchy of the communities, and variable node robustness are all observed, providing insights into the structure of the network.

Concepts: Scientific method, Structure, Hierarchy, Graph theory, Academic degree, Networks, Subroutine, Social network


In a number of applications there is a need to determine the most likely pedigree for a group of persons based on genetic markers. Adequate models are needed to reach this goal. The markers used to perform the statistical calculations can be linked and there may also be linkage disequilibrium (LD) in the population. The purpose of this paper is to present a graphical Bayesian Network framework to deal with such data. Potential LD is normally ignored and it is important to verify that the resulting calculations are not biased. Even if linkage does not influence results for regular paternity cases, it may have substantial impact on likelihood ratios involving other, more extended pedigrees. Models for LD influence likelihoods for all pedigrees to some degree and an initial estimate of the impact of ignoring LD and/or linkage is desirable, going beyond mere rules of thumb based on marker distance. Furthermore, we show how one can readily include a mutation model in the Bayesian Network; extending other programs or formulas to include such models may require considerable amounts of work and will in many case not be practical. As an example, we consider the two STR markers vWa and D12S391. We estimate probabilities for population haplotypes to account for LD using a method based on data from trios, while an estimate for the degree of linkage is taken from the literature. The results show that accounting for haplotype frequencies is unnecessary in most cases for this specific pair of markers. When doing calculations on regular paternity cases, the markers can be considered statistically independent. In more complex cases of disputed relatedness, for instance cases involving siblings or so-called deficient cases, or when small differences in the LR matter, independence should not be assumed. (The networks are freely available at

Concepts: Statistics, Object-oriented programming, Networks, Bayesian inference, Bayesian probability, Bayes' theorem, Linkage disequilibrium, Haplotype


A number of centrality measures are available to determine the relative importance of a node in a complex network, and betweenness is prominent among them. However, the existing centrality measures are not adequate in network percolation scenarios (such as during infection transmission in a social network of individuals, spreading of computer viruses on computer networks, or transmission of disease over a network of towns) because they do not account for the changing percolation states of individual nodes. We propose a new measure, percolation centrality, that quantifies relative impact of nodes based on their topological connectivity, as well as their percolation states. The measure can be extended to include random walk based definitions, and its computational complexity is shown to be of the same order as that of betweenness centrality. We demonstrate the usage of percolation centrality by applying it to a canonical network as well as simulated and real world scale-free and random networks.

Concepts: Algorithm, Real number, Graph theory, Networks, Computational complexity theory, Social network, Centrality, Network topology


Previous studies indicated that the quality of tropical composts is poorer than that of composts produced in temperate regions. The aim of this study was to test the type of manure, the use of co-composting with green waste, and the stabilization method for their ability to improve compost quality in the tropics. We produced 68 composts and vermicomposts that were analysed for their C, lignin and NPK contents throughout the composting process. Bayesian networks were used to assess the mechanisms controlling compost quality. The concentration effect, for C and lignin, and the initial blend quality, for NPK content, were the main factors affecting compost quality. Cattle manure composts presented the highest C and lignin contents, and poultry litter composts exhibited the highest NPK content. Co-composting improved quality by enhancing the concentration effect, which reduced the impact of C and nutrient losses. Vermicomposting did not improve compost quality; co-composting without earthworms thus appears to be a suitable stabilization method under the conditions of this study because it produced high quality composts and is easier to implement.

Concepts: Tropics, Bayesian network, Networks, Bayesian probability, Humus, Compost, Composting, Vermicompost