Dataset Information

Contact Trees: Network Visualization beyond Nodes and Edges.

ABSTRACT: Node-Link diagrams make it possible to take a quick glance at how nodes (or actors) in a network are connected by edges (or ties). A conventional network diagram of a "contact tree" maps out a root and branches that represent the structure of nodes and edges, often without further specifying leaves or fruits that would have grown from small branches. By furnishing such a network structure with leaves and fruits, we reveal details about "contacts" in our ContactTrees upon which ties and relationships are constructed. Our elegant design employs a bottom-up approach that resembles a recent attempt to understand subjective well-being by means of a series of emotions. Such a bottom-up approach to social-network studies decomposes each tie into a series of interactions or contacts, which can help deepen our understanding of the complexity embedded in a network structure. Unlike previous network visualizations, ContactTrees highlight how relationships form and change based upon interactions among actors, as well as how relationships and networks vary by contact attributes. Based on a botanical tree metaphor, the design is easy to construct and the resulting tree-like visualization can display many properties at both tie and contact levels, thus recapturing a key ingredient missing from conventional techniques of network visualization. We demonstrate ContactTrees using data sets consisting of up to three waves of 3-month contact diaries over the 2004-2012 period, and discuss how this design can be applied to other types of datasets.

SUBMITTER: Sallaberry A

PROVIDER: S-EPMC4718622 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Contact Trees: Network Visualization beyond Nodes and Edges.

Sallaberry Arnaud A Fu Yang-chih YC Ho Hwai-Chung HC Ma Kwan-Liu KL

PloS one 20160119 1

Node-Link diagrams make it possible to take a quick glance at how nodes (or actors) in a network are connected by edges (or ties). A conventional network diagram of a "contact tree" maps out a root and branches that represent the structure of nodes and edges, often without further specifying leaves or fruits that would have grown from small branches. By furnishing such a network structure with leaves and fruits, we reveal details about "contacts" in our ContactTrees upon which ties and relations ...[more]

PMID: 26784350

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Project description:BackgroundSequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system.ResultsWe combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models.ConclusionThe evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as network-represented combinations, are power-law distributed. This evidences an inflationary mode of evolution where the system diversity; 1) expands continuously alternating vertical and gradual processes of phylogenetic divergence with episodes of modular, saltatory and reticulate evolution; 2) is governed by the intrinsic capability of distinct LTR retroelement host-communities to self-organize their phenotypes according to emergent laws characteristic of complex systems.ReviewersThis article was reviewed by Eugene V. Koonin, Eric Bapteste, and Enmanuelle Lerat (nominated by King Jordan).

Dataset Information

Contact Trees: Network Visualization beyond Nodes and Edges.

Publications

Contact Trees: Network Visualization beyond Nodes and Edges.

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