The disappearing Neanderthal Y chromosome

Over the last decade, developments in genetic sequencing, as well as in the successful extraction of DNA from increasingly older and even contaminated remains, have allowed our knowledge of ancient hominins to expand exponentially. But even with these advances, our understanding of the Y chromosome – the one responsible for sex determination in humans – has remained relatively restricted until now. In this month’s ‘Science Notes’, we explore the evolution of the Y chromosome in Neanderthals and Denisovans (an extinct subspecies of humans, who appear to have been concentrated in Asia during the Lower and Middle Palaeolithic).

Previously, Y-chromosome sequences for Neanderthals and Denisovans had been lacking, as almost all of those whose DNA had been assessed turned out to be female; the few males that have been identified did not yield enough DNA for Y-chromosome analysis. This changed recently, however, with the development of a new set of probes – designed by Martin Petr, a graduate student from the Max Planck Institute for Evolutionary Anthropology.

Since Neanderthals, Denisovans, and modern humans are genetically quite similar to one another, short DNA probes based on the sequence of the modern human Y chromosome can be used to fish out Y chromosome sequences from DNA extracted from Neanderthal and Denisovan bones or teeth. The team from the Max Planck Institute used this technology to successfully retrieve Y chromosome DNA from two male Denisovans and three male Neanderthals.

One of the researchers on the project at work in the clean laboratory at the Max Planck Institute for Evolutionary Anthropology. Photo: Max Planck Institute for Evolutionary Anthropology.

This achievement has proved to be incredibly useful for understanding the evolution of these hominin groups. This is because, unlike autosomal DNA (which is inherited from both parents), the Y chromosome is inherited in a sex-dependent way: it is only passed on from a father to his sons. By examining its evolution, it is possible to trace the paternal lineage and also to discern shifts in sex-specific migration (that is, whether a group is practising matrilocality or patrilocality, and so on).

Previous analysis of mitochondrial DNA (mtDNA), which is passed on by a mother to all of her offspring, had suggested that the earliest Neanderthals originally had mtDNAs which were very closely related to those of Denisovans. But, some time between 219,000 and 468,000 years ago, modern human mtDNA was introduced into Neanderthals and began replacing their original Denisovan-like mtDNA. It appears that around this time there was a significant ‘gene flow’ event, when a modern human woman mated with a Neanderthal man. Could the Y chromosome help us tell a similar story of interspecies integration?

The Denisovan Y-chromosome data was pretty straightforward. It showed that the Y chromosomes from the two Denisovans probably split from modern human lineage around 700,000 years ago. This is in line with the data from autosomal DNA, which also indicates that Denisovans split away from the line around this time.

The Neanderthal data was more complicated, though. It showed that, instead of being more similar to Denisovans – as is the case with their autosomal DNA – the Neanderthal Y chromosome looked more like that of modern humans. The team concluded that the most-plausible explanation for this discrepancy was that there was interbreeding between Neanderthals and very early modern humans. This led to the complete replacement of Neanderthal Y chromosomes by those of modern humans – in effect, the Neanderthal Y chromosome disappeared. The team estimated that this introgression probably occurred between 100,000 and 370,000 years ago, when early modern human men mated with Neanderthal women.

It is possible that this mixing was around the same time as the event that introduced modern human mtDNA into the Neanderthal gene pool. It is substantially older, however, than the mixing event that led to traces of Neanderthal DNA being present in modern humans today, which is estimated to have occurred between 50,000 and 70,000 years ago. Overall, it seems that there were at least two interbreeding events between Neanderthals and modern humans that occurred at quite different times: one before the major out-of-Africa movement of modern humans, and one after.