Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

Abstract

The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-thinking era. We show how relatively recent comers in this field of study, that is, sequence-similarity networks, genome networks, and gene families–genomes bipartite graphs, already allow for a significantly enhanced usage of molecular datasets in comparative studies. Analyses of these networks provide tools for tackling a multitude of complex phenomena, including the evolution of gene transfer, composite genes and genomes, evolutionary transitions, and holobionts.

Challenges of annotation and analysis in computer-assisted language comparison: A case study on Burmish languages

“…In contrast to approaches that are solely interested in the relations between different concepts (List et al 2013), we wish to investigate both the actual word forms in our data and the concepts which they denote. Bipartite networks, which are increasingly used to investigate molecular datasets in evolutionary biology (Corel et al 2016), provide an intuitive and simple structure for such a computer-assisted investigation. Bipartite networks are networks consisting of two types of nodes.…”

Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers)

“…In evolutionary biology they are used to study complex evolutionary processes , Corel et al 2016. They represent sequences as nodes and connections between nodes represent similarities which are usually determined from similarity scores exceeding a certain threshold (Alvarez-Ponce et al 2013).…”

Phylogenetics, Reticulation and Evolution

“…The occurrence of such anomalous clustering in the evolutionary history of species poses serious challenges to practitioners of phylogenetic analysis as they result in genomic regions with locally incongruent genealogies relative to the speciation patern. Thus, phylogenetic analyses should account for the reticulate component of evolution, especially now that whole genome sequencing provides unprecedented phylogenetic information across the web of life [8]. Here, we present genetic and genomic evidence indicating the evolutionary importance of reticulation in multicellular eukaryotes and summarize relevant reticulate issues and its bearings on phylogenetic practice.…”