A question came to me over email, and the questioner agreed to let me post the article here. How would the scientists here answer him?
I recently read a paper that states that many the ERV insertions do not match the accepted pattern of common decent. And that when they do match it’s because of the insertions are not at all random but very specific. So, do matching ERVs really provide evidence for common ancestry? Or do they often match because the insertions are in fact not random, but target very specific locations in the genome? I may be totally missing the point, I’m pretty new to this subject.
The relevant papers and articles are below.
“We performed two analyses to determine whether these 12 shared map intervals might indeed be orthologous. First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates. This is particularly relevant for the human/great ape lineage. For example, only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee. Our Southern analysis shows that human and orangutan completely lack PTERV1 sequence (see Figure 2A). If these sites were truly orthologous and, thus, ancestral in the human/ape ancestor, it would require that at least six of these sites were deleted in the human lineage. Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely (Figure S3).
Several lines of evidence indicate that chimpanzee and gorilla PTERV1 copies arose from an exogenous source. First, there is virtually no overlap (less than 4%) between the location of insertions among chimpanzee, gorilla, macaque, and baboon, making it unlikely that endogenous copies existed in a common ancestor and then became subsequently deleted in the human lineage and orangutan lineage. Second, the PTERV1 phylogenetic tree is inconsistent with the generally accepted species tree for primates, suggesting a horizontal transmission as opposed to a vertical transmission from a common ape ancestor. An alternative explanation may be that the primate phylogeny is grossly incorrect, as has been proposed by a minority of anthropologists.”
“Endogenous retroviruses may arise within genomes by at least two different mechanisms: retrotransposition from a pre-existing endogenous retrovirus (intraspecific transmis- sion) or infection and integration via an exogenous source virus (horizontal transmission). Many cross-species trans- missions have been documented and frequently manifest themselves as inconsistencies in the presumed phylogeny of closely related species . During the 1970s and 1980s, Benve-niste and colleagues identified, by DNA hybridization and immunological cross-reactivity, several retroviral elements that could be found among more diverse primate/mammalian species but not necessarily among more closely related sister taxa [12,13,14]. Lieber and colleagues, for example, reported the isolation of a particular class of type C retroviruses from a woolly monkey (SSV-SSAV) and gibbon ape (GALV) but not the African great apes . These viruses shared antigenic properties with previously described type C activated endogenous retroviruses of the Asian feral mouse Mus caroli. Cross-species infection from murines to primates was proposed as the likely origin of the retrovirus. A related endogenous retrovirus was subsequently identified in the koala, suggesting a zoonotic transmission from placentals to mammals . Evidence of horizontal transmission for other families of retrovirus has been reported among classes of species as distantly related as avians and mammals.”