I might be missing something really obvious here but this study seems to be saying that 8 of the 131 ERV insertions are shared by rhesus macaque and humans, but not ANY of the intermediate 4 primate species. It can’t be due to ILS because , as far as I’m aware, the LCA with OW monkeys was 12 MY prior to the LCA of Great apes with gibbon. The paper does mention rearrangements and deletions which could account for a missing insertion in one species. I’m not sure though how 8 insertion could go “missing” in ALL 4 species that are more closely related to humans than rhesus macaque, but still be shared by rhesus macaque and humans. The paper says (pg. 4):
“The absence of an entire ERV-W insertion in some primates could be due to an integration having occurred after the separation of the respective evolutionary lineages, thus providing direct information on the time period of germ line colonization. It could however also depend on dele- tions, rearrangements, errors in genome sequence assem- blies or in their comparative analysis, particularly for primate species with less complete assemblies.
Based on our analysis, 123 out of 211 (H)ERV-W loci are actually shared by all analyzed Catarrhini primates, from human to Rhesus. However, when considering also the (H)ERV-W loci found in Rhesus and human but apparently absent in some intermediate primates (see above), the number of shared ERV-W loci increases to 131/211 (Fig. 2).”
My reading is derailed by their apparent belief, which the editors didn’t catch either, that all taxonomic names are italicized. Trivial point, but it’s consistent throughout the paper and it grates on me.
“The absence of an entire ERV-W insertion in some primates could be due to an integration having occurred after the separation of the respective evolutionary lineages, thus providing direct information on the time period of germ line colonization. It could however also depend on deletions, rearrangements, errors in genome sequence assemblies or in their comparative analysis, particularly for primate species with less complete assemblies.
Based on our analysis, 123 out of 211 (H)ERV-W loci are actually shared by all analyzed Catarrhini primates, from human to Rhesus. However, when considering also the (H)ERV-W loci found in Rhesus and human but apparently absent in some intermediate primates (see above), the number of shared ERV-W loci increases to 131/211 (Fig. 2).”
If the 211 insertions in humans 131 were found in Rhesus M. 8 of those 131 were only in humans and Rhesus M.
The paper’s wording is a bit confusing, it makes it seem like the primates are intermediate between humans and Rhesus. They’re not, as it explains in the next 2 sentences.
”Those findings corroborate the view that the first and major wave of ERV-W loci formation occurred between 43 and 30 MYa, after the separation of Catarrhini and Platyrrhini, but before the divergence of Rhesus lineage from Hominoidea, in line with previously reported integration periods [44, 46, 50].”
So, humans and all Catarrhini primates share 123 loci, while humans and the Rhesus lineage, which diverged more recently, share 131.
Yeah. I know there not intermediate, but Rhesus diverged 12 MY before gibbon and Great apes. So why are 8 insertions found in humans and Rhesus but not Gibbon, Orangutan, Gorilla and Chimpanzee but not human?
The Rhesus lineage is the earliest diverging lineage within Catarrhini. The “intermediate primates” are the gibbon, orangutan, gorilla, and chimp, which all diverged later than the Rhesus.
when considering also the (H)ERV-W loci found in rhesus and human but apparently absent in some intermediate primates
So those 8 insertions are each missing in one or more of the intermediate 4 primate species, not all of them. You can see the raw data in Table S1, which you can download here.
In this table, I’ve isolated the rows containing the 8 ERVs in question - the ones shared between humans and rhesus but missing in one of the intermediate species.
You can see that in 7 out of the 8 cases, the ERV is missing in a single intermediate species (1 missing in gorilla, 5 missing in gibbon, and 1 in chimpanzee). In the 8th case (row 3), it seems to be missing in chimp, gorilla, and gibbon but present in human, orangutan, and rhesus.
That doesn’t say what you think it does. Your reading is that the loci are found in Rhesus and human but absent in all “intermediate” primates. But the quote says “some”. A locus found in Rhesus, human, chimp, orangutan, and gibbon but not in Gorilla would qualify. i will admit that much of this paper is poorly written and confusing. I merely speculate on what the authors mean by “intermediate”, and I don’t know what “see above” refers to either. But your reading is clearly incorrect.
This should be easy to determine from the sequences, since ERVs should very seldom be excised exactly, leaving the flanking sequences intact as if there had been no insertion. Same for independent insertions in exactly the same spot. Mind you, it has happened a few times that I’m aware of.
You would have to check the flanking sequences. But I’m not sure what the difference is. Unequal recombination is one form of deletion. The real question is whether we have a deletion or independent insertions. A deletion is unlikely to be exact, leaving no remnant of the ERV and also leaving the flanking sequences intact, as if there had been no insertion at all. (But that has occasionally happened.)
