There is a paradox for RNA virus origin. Because the high mutation rate of these viruses, the large genetic distance between two unrelated viruses can be arrived at in very short time frames, like less than 100,000 years. This is a challenge to the molecular clock but is evidence for the MGD hypothesis. Two viruses may share a common ancestor many million years ago but their genetic distance would reach a maximum in less than 100000 years and stays unchanged forever thereafter.
Some genes like proteases are conserved in viruses and all cellular life forms. In such genes, the genetic distance between two closely related and recently separated viuses, like HIV1 and HIV2, is equivalent to that between bacteria and eukaryia representing 2 billion years of separation. So, simple life forms can reach great genetic distance in very short time. Genetic distance between evolutionally distant viruses represents the maximum.
Are RNA viruses adapting or merely changing?
J Mol Evol. 2000 Jul;51(1):12-20.
Sala M, Wain-Hobson S.
Molecular Clocks and the Puzzle of RNA Virus Origins
Journal of Virology, April 2003, p. 3893-3897, Vol. 77, No. 7
Edward C. Holmes
Although the ultimate origins of RNA viruses are uncertain, it seems reasonable to assume that these infectious agents have a long evolutionary history, appearing with, or perhaps before, the first cellular life-forms (38). While the RNA viruses we see today may not date back quite this far, the evidence that some DNA viruses have evolved with their vertebrate hosts over many millions of years (24) makes an equally ancient history for RNA viruses a natural expectation. Yet a very different picture of RNA virus origins is painted if their gene sequences are compared; by using the best estimates for rates of evolutionary change (nucleotide substitution) and assuming an approximate molecular clock (21, 33), it can be inferred that the families of RNA viruses circulating today could only have appeared very recently, probably not more than about 50,000 years ago. Hence, if evolutionary rates are accurate and relatively constant, present-day RNA viruses may have originated more recently than our own species.