The rather amazing links below describes the presence of integrated filovirus-like elements (filoviruses include the highly pathogenic Marburg and Ebola viruses) within the genomes of mammals and also unbelievably marsupials. Major conclusions are that viruses can integrate to genomic DNA without the requirement for reverse transcriptase (HIV can form a provirus unforunately and establish a recalcitrant reservoir) and that the filoviruses themselves are considerably more ancient than previously thought (tens of millions as opposed to tens of thousands of years). It also I believe provides evidence for what Frank Ryan (cf. Virolution http://www.amazon.co.uk/Virolution-Frank-Ryan/dp/0007315120) describes as "aggressive symbiosis" where viruses can co-evolve with humans and play a major role in evolution in terms of gene transfer and a type of genetic defence. Examples of these aggressive symbiotic reataionships include the pox viruses in American grey squirrels leading to the likely extinction of the red squirrel in the near future, the introduction of myxomatosis in rabbits in Australia and SIV and the herpesviruses in primates. Evolution appears not be linear but reticulated in form with a great deal of horizontal gene transfer occurring so a tree of life is probably an erroneous view as Darwin scribbled in that famous picture (http://www.age-of-the-sage.org/evolution/charles_darwin/charles-darwin-tree-of-life-sketch-1837.jpg) and life's relationships are more likely similar to a tree covered with a net.
BMC Evol Biol. 2010 Jun 22;10(1):193. [Epub ahead of print]
Filoviruses are ancient and integrated into mammalian genomes.
Taylor DJ, Leach RW, Bruenn J.
ABSTRACT: BACKGROUND: Hemorrhagic diseases from Ebolavirus and Marburgvirus (Filoviridae) infections can be dangerous to humans because of high fatality rates and a lack of effective treatments or vaccine. Although there is evidence that wild mammals are infected by filoviruses, the biology of host-filovirus systems is notoriously poorly understood. Specifically, identifying potential reservoir species with the expected long-term coevolutionary history of filovirus infections has been intractable. Integrated elements of filoviruses could indicate a coevolutionary history with a mammalian reservoir, but integration of nonretroviral RNA viruses is thought to be nonexistent or rare for mammalian viruses (such as filoviruses) that lack reverse transcriptase and replication inside the nucleus. Here, we provide direct evidence of integrated filovirus-like elements in mammalian genomes by sequencing across host-virus gene boundaries and carrying out phylogenetic analyses. Further we test for an association between candidate reservoir status and the integration of filoviral elements and assess the previous age estimate for filoviruses of less than 10,000 years. RESULTS: Phylogenetic and sequencing evidence from gene boundaries was consistent with integration of filoviruses in mammalian genomes. We detected integrated filovirus-like elements in the genomes of bats, rodents, shrews, tenrecs and marsupials. Moreover, some filovirus-like elements were transcribed and the detected mammalian elements were homologous to a fragment of the filovirus genome whose expression is known to interfere with the assembly of Ebolavirus. The phylogenetic evidence strongly indicated that the direction of transfer was from virus to mammal. Eutherians other than bats, rodents, and insectivores (i.e., the candidate reservoir taxa for filoviruses) were significantly underrepresented in the taxa with detected integrated filovirus-like elements. The existence of orthologous filovirus-like elements shared among mammalian genera whose divergence dates have been estimated suggests that filoviruses are at least tens of millions of years old. CONCLUSIONS: Our findings indicate that filovirus infections have been recorded as paleoviral elements in the genomes of small mammals despite extranuclear replication and a requirement for cooption of reverse transcriptase. Our results show that the mammal-filovirus association is ancient and has resulted in candidates for functional gene products (RNA or protein).