Hello, I am working with closely related endogenous retrovirus (ERV) sequences. I suspect these might have been the result of several integration events from different but related exogenous retroviruses according to host phylogeny and geography. Basically, distant hosts that share geographical distribution have higher ERV identity between theirs than with closer species. ERVs from a single species that is closely related to a few others and has the same habitat, is however very different from its neighbors.
So two possibilities: each ERV clade comes from a different virus or all of them descend from the same insertion event.
But it remains as a hunch. Is there some sort of statistical test or other kind of test that might at least support or oppose this claim?
Thank you in advance.
I think it would depend a bit on the distances you are discussing. The exogenous retroviral genomes evolve roughly ten million-fold faster than the mammal host DNA. So exogenous virus that entered different host lines to become endogenous something like 100 years apart in time could be quite distant from each other.
The endogenous retroviruses of humans, chimpanzees, gorillas, orangutans, gibbons, etc have been studied in quite some detail, so you can use them as a good example to see the types of distances observed between the endogenous viruses and the hosts. Most of them are called "HERVs" for "Human Endogenous Retroviruses" but are in fact primate endogenous retroviruses and not unique to the human lineage.
The location in the host genome is also a major clue as to the timing of the integration event(s). Most endogenous retroviruses can and do move from one location to another (or get copied from one location to additional locations) over time. But when we see a retroviral genome in the exact same site on the same chromosome in chimpanzee and human, we can be essentially certain it integrated into the chimp/human lineage before the lineage leading to humans split from the lineage leading to chimpanzees.
https://pubmed.ncbi.nlm.nih.gov/?term=human+chimpanzee+orangutan+endogenous+retrovirus
Brings up 24 publications, while the same search for just human and chimpanzee without orangutan brings up 90 publications.
The fossil record for great apes and hominids has been quite carefully studies, but there is still a lot of uncertainty about how often various hominid ancestors may have passed through the forests where chimpanzee and gorilla ancestors lived over the past 8 million years or so.
https://pubmed.ncbi.nlm.nih.gov/24262833/
Has a good discussion of movement of endogenous retroviruses in fairly recent times (less than 1 million years) in the Neanderthal, Denisova and modern human genomes.
Thank you for your answer, unfortunately, the taxa I am studying are less studied and species are more distant (20+ my). Checking chromosomal locations among taxa that are not as well studied as Primates goes outside the scope of the paper, plus, the contigs we have located ERVs in are sometimes unplaced in the genome. We have been told by other sources that we might need to do nearest neighbor analysis or a maximum likelihood statistical test.
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