Great! Now show some ancient or even quite old sapien genome examples where specific ones are not present and then they are...so we can see they ARE actual insertions....a few comparative examples from the ones shared should suffice.
Neandertal and Denisovan retroviruses
Lorenzo Agoni, Aaron Golden, Chandan Guha, Jack Lenz
Open Archive DOI:
http://dx.doi.org/10.1016/j.cub.2012.04.049
Summary:
Modern humans (Homo sapiens) last shared a common ancestor with two types of archaic hominins, Neandertals and Denisovans, roughly 800,000 years ago, and the population leading to modern H. sapiens separated from that leading to Neandertals and Denisovans roughly 400,000 years ago [1–4] . Genome sequences for these two types of archaic hominins have been reported [1,2] . They were determined by sequencing ancient DNAs using techniques that generated many short sequence reads. Here, we analyzed individual sequence reads used to assemble the published Neandertal and Denisovan genomes for insertions of Human Endogenous Retrovirus K (HERV-K) DNA.
Virus–host DNA junctions were identified that defined 14 proviruses where modern humans contain the corresponding, empty, preintegration site. Thus, HERV-K reinfected germ lineage cells of Neandertals and Denisovans multiple times, and these events occurred around the time of or subsequent to the divergence of the archaic hominin lineages from that leading to modern humans. One of the proviruses was shared by Neandertals and Denisovans, which is consistent with the hypothesis that these archaic humans shared a common ancestor more recently than they shared one with the lineage leading to modern humans.
HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses
Rafael Contreras-Galindo, Mark H. Kaplan, Shirley He, Angie C. Contreras-Galindo, Marta J. Gonzalez-Hernandez, Ferdinand Kappes, Derek Dube1, Susana M. Chan, Dan Robinson, Fan Meng, Manhong Dai, Scott D. Gitlin, Arul M. Chinnaiyan, Gilbert S. Omenn and David M. Markovitz
Abstract:
Human endogenous retroviruses (HERVs) make up 8% of the human genome. The HERV-K (HML-2) family is the most recent group of these viruses to have inserted into the genome, and we have detected the activation of HERV-K (HML-2) proviruses in the blood of patients with HIV-1 infection. We report that HIV-1 infection activates expression of a novel HERV-K (HML-2) provirus, termed K111, present in multiple copies in the centromeres of chromosomes throughout the human genome yet not annotated in the most recent human genome assembly. Infection with HIV-1 or stimulation with the HIV-1 Tat protein leads to the activation of K111 proviruses. K111 is present as a single copy in the genome of the chimpanzee, yet K111 is not found in the genomes of other primates.
Remarkably, K111 proviruses appear in the genomes of the extinct Neanderthal and Denisovan, while modern humans have at least 100 K111 proviruses spread across the centromeres of 15 chromosomes. Our studies suggest that the progenitor K111 integrated before the Homo-Pan divergence and expanded in copy number during the evolution of hominins, perhaps by recombination. The expansion of K111 provides sequence evidence suggesting that recombination between the centromeres of various chromosomes took place during the evolution of humans. K111 proviruses show significant sequence variations in each individual centromere, which may serve as markers in future efforts to annotate human centromere sequences. Further, this work is an example of the potential to discover previously unknown genomic sequences through the analysis of nucleic acids found in the blood of patients.
