Hi @dcscccc -
I suspect you did not read the entire article by Barbulescu et al. Here are the details you missed:
In principle, the following gene conversion scenario could have resulted in the removal of the provirus in the human lineage. First, the preintegration locus underwent a duplication event in the common ancestor of Homo, Pan, and Gorilla. Second, the provirus formed in one of the two copies of the locus by viral infection of the common ancestor. Next, the Gorilla lineage diverged from the Pan-Homo common ancestor. Then, the Pan and Homo lineages diverged. Afterwards, a recombination event reversed the original locus duplication, restoring a single copy of the locus without the provirus in the Homo lineage. However, the PCR and sequencing assays uniformly failed to detect any evidence for the presence of such a duplicated locus in Gorilla or Pan. Therefore, in addition to the removal of the provirus specifically in the Homo lineage, the scenario also requires recombination events in the Pan and Gorilla lineages to eliminate the provirus-free copy of the locus. Since the Gorilla lineage diverged before the Pan and Homo lineages separated, this means that independent recombination events would have had to occur in both the Pan and Gorilla lineages. While this scenario can never be formally excluded, there is a more parsimonious alternative that involves three fewer recombination events.
The alternative is an allelic segregation model (Figure 2d) in which the provirus formed in the most recent common ancestor of Homo, Pan, and Gorilla just before the three lineages separated. The provirus allele was fixed in the Gorilla lineage. Both alleles were then maintained in the Pan-Homo common ancestor until the individual lineages diverged. The provirus allele was fixed in the Pan lineage, while the preintegration site allele was fixed in the Homo lineage. The allelic segregation model is more parsimonious than the gene conversion scenario because it does not require the locus duplication event in the common ancestor or the two independent losses of the duplicated locus in the Gorilla and Pan lineages. In addition, the possibility that humans diverged first, the provirus formed next, and the gorilla-chimpanzee divergence occurred last is extremely unlikely given the greatest sequence similarity between chimpanzees and humans at most loci [1, 2, 3, 4]. Rather, the presence of HERV-K-GC1 in gorillas and chimpanzees, but not humans, is best explained by the maintenance of the preintegration site in the human lineage since before the time when the provirus formed in the common ancestor of chimpanzees and gorillas. This leads to the conclusion that, for some fraction of the genome, the gorilla and chimpanzee genomes are more closely related to each other than either is to humans.
Yes, Barbulescu et al. state that incomplete lineage sorting is the best, most parsimonious explanation of the genetic data. You only call the primate phylogeny “a good joke” because you have not yet understood incomplete lineage sorting in spite of the efforts of many of your friends here. But I believe you can if you will just try: Dennis Venema gave a very clear and helpful explanation in this Biologos article.
Grace and peace,
Chris Falter