CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection.

Genes evolve by point mutations, but also by shuffling, fusion, and fission of genetic fragments. Therefore, similarity between two sequences can be due to common ancestry producing homology, and/or partial sharing of component fragments. Disentangling these processes is especially challenging in large molecular data sets, because of computational time.

Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics.

Background: For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today.

Bipartite graph analyses reveal interdomain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins.

Based on their small size and genomic properties, ultrasmall prokaryotic groups like the Candidate Phyla Radiation have been proposed as possible symbionts dependent on other bacteria or archaea. In this study, we use a bipartite graph analysis to examine patterns of sequence similarity between draft and complete genomes from ultrasmall bacteria and other complete prokaryotic genomes, assessing whether the former group might engage in significant gene transfer (or even endosymbioses) with other community members. Our results provide preliminary evidence for many lateral gene transfers with other prokaryotes, including members of the archaea, and report the presence of divergent, membrane-associated proteins among these ultrasmall taxa.