The dual-origin hypothesis of viruses under environmental stress and energy crisis.

The origin of viruses is one of the central mysteries in evolutionary biology. Although mainstream hypotheses such as "reduction," "escape," and "virus-first" exist, they each face significant difficulties in explaining the motivation for establishing viral parasitism, the origin of the capsid, and the minimalism of RNA viruses. This paper aims to propose a new model named the "environmentally driven coordinated reduction" model, intended to provide a logical framework with a clear environmental driving mechanism for the "polyphyletic" origin of viruses, particularly the "reduction pathway." This model posits that an emergency dormancy program initiated by ancient prokaryotes to cope with extreme environmental conditions on the surface of the primitive ocean-including the active disassembly of organelles, streamlining of the genome, and the formation of multi-layered protective capsids-constituted the initial driving force for viral reduction. These "dormant bodies," upon returning to suitable environments and having lost the capacity for independent survival, saw the release of their genetic material passively evolve into parasitic infection. This model not only proposes an origin pathway for DNA viruses but also innovatively places the origin of RNA viruses as a secondary simplification product, resulting from a reversion to a more energy-efficient RNA system under energy depletion pressure, thereby naturally incorporating minimal molecules like viroids into the endpoint of its evolutionary path. In particular, this paper explicitly identifies the last universal common ancestor (LUCA) and its direct descendants as the primary source of viral evolution. The large gene pool possessed by LUCA not only provided a dispensable gene set as an energy reserve, but also significantly extended the maximum dormancy period of cells under extreme environments through the effect of genomic redundancy, thereby exponentially increasing the probability of the viralization transition. This mechanism is rigorously demonstrated through mathematical models in Chapter 7, revealing the quantitative relationship between LUCA's large genome and the probability of viral origin. Through a critical hypothetical review, this paper systematically analyzes the shortcomings of these classic hypotheses and, on this basis, provides a logical framework for a unified picture of viral origins, ultimately proposing specific predictions testable by computational biology and experimental evolutionary biology.