Comparison of modern human and Neanderthal skulls from the Cleveland Museum of Natural History.
We know Neanderthals left their mark on the DNA of many modern humans, but this exchange has worked both ways. The groups of Neanderthals that our species encountered in Eurasia about 45,000 years ago already carried some Homo sapiens genes as mementos of much earlier encounters. A recent study suggests that these early encounters enabled the Homo sapiens version of the Y chromosome to completely replace the original Neanderthal version 370,000 to 100,000 years ago.
Evolutionary geneticists Martin Petr, Janet Kelso, and their colleagues used a new method to sequence Y chromosomal DNA from two Denisovans and three Neanderthals from locations in France, Russia, and Spain (all three lived 38,000 to 53,000 years ago). The oldest Neanderthal genomes in Eurasia have Y chromosomes that are much more similar to those of Denisovans. Later Neanderthals, however, have Y chromosomes that are more similar to those of us humans.
The gene flow is a one-way street
Tens of thousands of years ago, our species shared the world with at least two other hominins. The tools, beads, and art they left behind suggest that these other people were likely very much like us. And we were definitely all alike enough to seemingly have some sex.
This resulted in a really complicated population history that spanned thousands of years and several continents. We met the daughter of a Neanderthal and a Denisovan in the archaeological record, and the DNA of our species documents ancient encounters with Neanderthals and Denisovans. And Neanderthal genomes also carry the genetic legacy of much earlier encounters with early Homo sapiens.
Most of what we know comes from the DNA of our regular chromosomes – there is less data on sex chromosomes. Geneticists can use the differences in this DNA to estimate when two populations like Homo sapiens and Neanderthals last shared a common ancestor. Count the small differences in their DNA and compare them to how quickly human DNA mutations accumulate. You can think of an approximate date for dividing the populations. (Take a second to understand how cool it is that we actually know this.)
The DNA data we have on the nonsex chromosomes shows that Neanderthals and Denisovans share a branch of the human family tree that split off from our branch 700,000 to 550,000 years ago. But the Y chromosomes tell a different story, suggesting that our youngest common ancestor lived about 370,000 years ago.
This suggests that long after the groups went their separate ways and evolved into different populations, the groups met and exchanged genes (which, of course, they definitely called that back then). Over time, our version of the Y chromosome genome replaced the Neanderthal version.
“A big advantage of (studying) Y chromosomes and mitochondrial DNA is that while they only provide a simple overview of human history through a single paternal / maternal line, they can highlight some aspects of it (such as gene flow) clearer, "said Petr and Kelso to Ars." This is the case with the gene flow of people of the early modern age in Neanderthals, which emerges from our study, which is extremely clear. Finding something like this in autosomal DNA is much more difficult and requires sophisticated statistical methods (which are now finally being developed). "
A slight evolutionary edge
There's a reason non-African people only have a tiny number of Neanderthal alleles – around two to four percent – in their genome these days. When two groups like Homo sapiens and Neanderthals mix, alleles from both parents are passed on to their offspring. However, the chances are good that an allele from one group will be “fixed” in the gene pool of the other group (meaning that it will become the dominant form). First, the new allele must be passed on to a sufficiently large percentage of the offspring, which rarely happens unless there is extensive intermingling over time.
But things can be different when the new allele has natural selection on its side. If the new allele somehow makes it more likely that a person will pass on their genes to a new generation (or if it's linked to another gene that does), it is likely to persist.
Previous studies showed that our species' alleles likely made their way into the Neanderthal gene pool at a relatively low rate: roughly a single-digit percentage of the population. That's not enough to be repaired. Petr, Kelso, and their colleagues therefore suggest that the Homo sapiens Y chromosome alleles are likely to offer a fitness benefit compared to the Neanderthal versions.
"This is the model that we propose for replacement as a purely random alternative to replacement without resorting to natural selection (which is rather unlikely)," Petr and Kelso told Ars. How much difference does a tiny selective advantage really make? They carried out a computer simulation in which a Y chromosome allele of Homo sapiens was passed on to only five percent of the Neanderthal population in a single admixture. When the simulation increased the fitness benefit of this allele by just one percent, the chances of replacing the older Neanderthal version over 50,000 years rose to about 25 percent.
That suggests that Selective Edge Homo sapiens alleles may have been tiny, but that's enough to stay.
Older DNA, please
There is currently not enough information for an archaeologist or geneticist to say what selective benefit was written into Homo sapiens Y chromosomal DNA. To understand this, we need more Denisovan and Neanderthal genomes – and especially more Y chromosomes, which were rare until recently. So far, the handful of Neanderthals and Denisovans with the best-preserved genomes have been found to be female.
"It's really just a random chance. So far we have genomes with high coverage of three Neanderthals and one Denisovan. The likelihood that they are all female is actually not that small," they said. Petr, Kelso, and their colleagues had to use a newly developed DNA extraction method to get enough Y chromosomal DNA from their samples to actually study.
They also used the method on a 46,000 to 53,000 year old Neanderthal man from El Sidron Cave, Spain, whose genome had previously been sequenced. The new method has helped revise an earlier estimate of the most recent common ancestor of the Neanderthal Y chromosome with our species, which shows why it is sometimes important to re-examine old specimens using new methods. But we also need more Neanderthal and Denisovan genomes to fill in the details of their history.
"The most obvious step is to sequence more archaic human Y chromosomes, especially those from older Neanderthals than those analyzed in our study, and also those from a wider range of known Neanderthals (all three Neanderthals in our study are from Western Eurasia ). " Petr and Kelso told Ars, "This will help us narrow down the timing of the swap and test how far the Y chromosome replacement has geographically spread."
They added: “Having access to Y chromosomes with high coverage of Neanderthal (and also Denisovan) Y chromosomes prior to introgression will allow us to look beyond the theoretical simulations in our current study to identify which selection drivers are stand behind the replacement. ”
Science, 2020 DOI: 10.1126 / 10.1126 / science.abb6460 (About DOIs).