Viruses and mobile genetic elements are molecular parasites or symbionts that 
coevolve with nearly all forms of cellular life. The route of virus replication 
and protein expression is determined by the viral genome type. Comparison of 
these routes led to the classification of viruses into seven "Baltimore classes" 
(BCs) that define the major features of virus reproduction. However, recent 
phylogenomic studies identified multiple evolutionary connections among viruses 
within each of the BCs as well as between different classes. Due to the modular 
organization of virus genomes, these relationships defy simple representation as 
lines of descent but rather form complex networks. Phylogenetic analyses of 
virus hallmark genes combined with analyses of gene-sharing networks show that 
replication modules of five BCs (three classes of RNA viruses and two classes of 
reverse-transcribing viruses) evolved from a common ancestor that encoded an 
RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses 
evolved from this ancestor on multiple, independent occasions via the 
recruitment of distinct cellular proteins as capsid subunits and other 
structural components of virions. The single-stranded DNA (ssDNA) viruses are a 
polyphyletic class, with different groups evolving by recombination between 
rolling-circle-replicating plasmids, which contributed the replication protein, 
and positive-sense RNA viruses, which contributed the capsid protein. The 
double-stranded DNA (dsDNA) viruses are distributed among several large 
monophyletic groups and arose via the combination of distinct structural modules 
with equally diverse replication modules. Phylogenomic analyses reveal the finer 
structure of evolutionary connections among RNA viruses and reverse-transcribing 
viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, 
these analyses allow us to outline the global organization of the virus world. 
Here, we describe the key aspects of this organization and propose a 
comprehensive hierarchical taxonomy of viruses.