A Place for Viruses on the Tree of Life

Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). However, there can be no doubt that viruses play a significant role in evolution, the force that facilitates all life on Earth. Conceptually, viruses are regarded by many as non-living entities that hijack living cells in order to propagate. A strict separation between living and non-living entities places viruses far from the ToL, but this may be theoretically unsound. Advances in sequencing technology and comparative genomics have expanded our understanding of the evolutionary relationships between viruses and cellular organisms. Genomic and metagenomic data have revealed that co-evolution between viral and cellular genomes involves frequent horizontal gene transfer and the occasional co-option of novel functions over evolutionary time. From the giant, ameba-infecting marine viruses to the tiny Porcine circovirus harboring only two genes, viruses and their cellular hosts are ecologically and evolutionarily intertwined. When deciding how, if, and where viruses should be placed on the ToL, we should remember that the Tree functions best as a model of biological evolution on Earth, and it is important that models themselves evolve with our increasing understanding of biological systems.

Viruses infect all cellular life. Their evolution is inextricably bound to their target cells. Whether lyzing cells as part of a lytic cycle or inserting their DNA into the host genome in the lysogenic cycle, viruses place selective pressure on cells to evolve counter measures to evade infection. This, in turn, forces the virus to evolve further to avoid the defensive strategies of the host. A dynamic and long-standing co-evolution stems from the ecological interactions of viruses with host cells. These interactions have traditionally been viewed as predatory and simply favor viral replication, but research into the effect of bacteriophages on microbial populations indicates that viruses may well be essential for ecosystem diversity .

Viruses lack a ribosome, preventing them from making their own proteins. Instead, they use the host cellular machinery to translate their messenger RNA (mRNA) into proteins, allowing them to assemble and multiply .Virus genomes are composed of either DNA or RNA and can be single-stranded (ss) or double-stranded (ds). They are divided into seven Baltimore classes, which also include positive-strand (+ss) and negative-strand (-ss) RNA viruses as well as two classes of retrovirus.Recently, a proposed megataxonomy of the virus world has placed viruses in a hierarchical taxonomic structure similar to that of cellular life.Almost all viruses encode capsid proteins that enclose and protect their genetic material; an exception to this is satellite viruses that rely on other viruses for their encapsidation .

The standard ToL can be viewed as a two-dimensional, bifurcating species tree with a root representing the last universal common ancestor (LUCA). Diversity is usually plotted on the x-axis and time (or evolutionary rate) on the y-axis. The prevalence of horizontal gene transfer (HGT) in prokaryotes has already cast doubt on this simplistic model .It is important to remember that macroscopic lifeforms are the exception rather than the rule when we consider the number of species on this planet. The Open ToL is an online initiative to maintain a comprehensive, dynamic, and digital species ToL that, at its outset, included 2.3 million species .We can only imagine how sophisticated and multi-dimensional such a digital model could be in principle, albeit not yet in practice.