An in-depth analysis of viral evolution gives evidence that they belong on the tree of life, despite long-held arguments for the contrary.
Viruses have been a thorn in the sides of scientists ever since their discovery. There’s the obvious reason — their insidious infections cause countless deaths and often evade cures — as well as a more academic conundrum — how should they be classified? Are they full-fledged living organisms, as complex as their infected victims, or merely fragments of genetic material and proteins that interact with life?
If we’re defining “life” as any structure that has its own genes and seeks to perpetuate those genes, viruses definitely fit the bill — anyone who has fought off a particularly nasty cold or flu has intimate experience with the stubborn survival skills of viruses. They also exhibit stunning diversity in structure and genome, and use very specific mechanisms to infect their hosts. This diversity results from the same forces of natural selection that operate on us and other lifeforms.
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Despite these qualities, many biologists still argue that viruses do not deserve a branch on the tree of life. While viruses technically reproduce, they depend on their hosts to do so. Unless they can get inside host cells and hijack the endemic cellular machinery for their own purposes, viruses cannot multiply. In fact, some scientists believe that viruses originally obtained all their DNA from host cells, making them more like rogue pieces of genetic material that have turned on their owners.
They also lack the strict cellular structure possessed by even the simplest bacteria. Instead of dividing, viruses autonomously assemble from their components. Aside from replicating their DNA and constituent proteins, viruses don’t perform any metabolic activities or require nutrients. Because of these limits on their lifelike behavior, they have instead been described as “organisms at the edge of life.”
But a new study has delved deep into the evolutionary history of viruses, and argues that their evolution has earned viruses a place among proper living organisms. Until now, drawing up this evolutionary history proved a difficult task because viruses proliferate within their hosts so rapidly. Each round of genetic replication comes with a load of mutations made while copying the DNA sequences, which become difficult to track through generations of viruses. The viral DNA also tends to mix in with host DNA, which further complicates the picture. Using DNA sequences, scientists have managed to identify fewer than 5,000 species, a tiny fraction of the millions that are estimated to exist.
So researchers at the University of Illinois decided to shift their focus to proteins instead of DNA. Specifically, they analyzed the folds that give proteins their 3D configurations and determine how they operate. Even if the genetic sequences that encode proteins acquire mutations, the proteins are less likely to accumulate changes that would disrupt their function. As such, the few structural changes that do occur can mark major changes in a virus’s evolutionary history.
The researchers sifted through the protein folds of over 5,000 organisms to track down 442 folds shared between cells and viruses, as well as 66 unique to viruses. The evolution of protein folds encoded by DNA sequences unlike any seen in living cells abolishes the theory that viruses took all their genetic material from hosts. This allowed the researchers to construct a tree of life showing the relationships between viruses and the cells from which they’ve borrowed DNA. They could also tease out families of viruses who shared the same unique protein folds inherited from a common ancestor.
The data ultimately suggests that viruses evolved from primitive ancient cells. They co-existed with the ancestors of modern cells, devising new strategies of attack against newly evolving defense mechanisms. Plenty of parasitic bacteria and fungi also need to get inside other cells before they can reproduce, and share coevolutionary relationships with their hosts that are just as ancient and complex. The researchers thus argue that dependency on host organisms doesn’t preclude viruses from the definition of life.