Well, some of you! And maybe me!
Last year, scientists combed through Neanderthal and Denisovian DNA sequences (yeah, those exist!) and found fourteen ERVs that were in Neanderthals and/or Denisovians, but NOT humans.
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 [1,2,3,4]. 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.
Remember, HERV-K ERVs are usually the ‘youngest’, thus the most likely to be polymorphic between humans, Neanderthals, and Denisovans. In humans, there was no evidence these 14 Neanderthal/Denisovan ERVs were ever there (not a broken ERV, not a solo LTR, just regular ol DNA sequence).
The conclusion was, was that these Neanderthal and/or Denisovan ERVs must have inserted themselves into their respective genomes after the ancient relatives/human split.
Speciation isnt a ‘clean’ break. Its not as if one day there is a human/Neanderthal/Denisovan ancestor, and the next day there are humans and Neanderthals and Denisovans.
Speciation is a time consuming, tangled up mess.
So this new information isnt surprising at all:
The human genome project, the human reference genome, does not contain the genomes of all humans. It contains the genomes of a select few humans.
These researchers hunted through the genetic sequences of individuals whos genomes were sequenced for other reasons (a cancer project) and they ended up finding most of the ‘absent’ ERVs! Not in every patient, but some patients had one, some patients had others, etc.
What does this mean?
With the exception of co-opted ERV loci such as syncytins , which could increase in frequency due to positive selection, we assume ERV loci become common by genetic drift, and the average time for a neutral allele to go to fixation is 4Ne generations (where Ne is the effective population size). Given estimates of long-term human generation time and population size , this is ∼800,000 years. The population divergence of modern humans from the Denisovan/Neanderthal lineage is more recent, between 170,000 and 700,000 years according to a more recent — and much deeper —sequencing of the above Denisovan fossil , so many loci will have persisted at fluctuating frequencies in all three lineages.
It means unless an ERV is really positive (and selected for) or really negative (and selected against), ERVs just drift. They will remain polymorphic in a population until a given number of generations, depending on the size of the population (that is, all humans have the same really old ERVs, these younger ERVs are different between humans).
So some of us have more in common with our Neanderthal and Denisovan ancient cousins than others.