Recent human ancestry remains a complex puzzle, although we are steadily filling in the pieces. For the first time scientists have looked at the Y chromosomes of modern humans, Neanderthals, and Denisovans, giving us yet one more piece of the puzzle. But first, here’s some background.

The common ancestor of humans (by which I mean modern humans), Neanderthals, and Denisovans lived between 500,000-800,000 years ago. This common ancestor species almost definitely lived in Africa, but we are not sure exactly which species it was. Homo heidelbergensis is a candidate, but it’s not clear if the timeline matches up well enough. In any case, this split probably occurred when the ancestors of Neanderthals and Denisovans migrated from Africa to Europe. They then split from each other, with the Neanderthals remaining in Europe and the Denisovans going to Asia. This split happened around 600,000 years ago, but could be more recent.

Why is there so much confusion about the exact time of the split? There are two main reasons. The first is that these splits were not single events. Populations of early humans became relatively separated from each other, enough so that genetic differences could start piling up. But they also continued to interbreed, sharing genes throughout their history. There is a specimen that is likely the child of a Neanderthal and a Denisovan from just 50,000 years ago. Humans and Neanderthals interbred right up until the end. All non-African humans living today have 2-3% Neanderthal DNA.

The other reason the divide is difficult to pin down is because there are numerous methods for estimating when it occurred, and they give slightly different answers. We can look at teeth, and other fossil bones, and genomic DNA, mitochondrial DNA, or specifically X and Y chromosomes. We can also look at their culture via their tools. We can see when certain tools start appearing in different locations. Culture, by the way, can also be shared among populations, so that picture may be confused as well.

The new study looks at the Y chromosomes of three male Neanderthals and two male Denisovans, comparing them to modern humans. Prior DNA analysis on Denisovans has been only on females, so this is the first look at their Y chromosome. The scientists were also employing a new technique that helps isolate this DNA from contaminating DNA, such as from bacteria. From everything I wrote above, and looking at the pictured diagram, you would expect that Neanderthals and Denisovans would have more similar Y chromosomes than either are to modern humans. That is what the scientists expected to see – but they didn’t. Rather they found that humans and Neanderthals have more similar Y chromosomes than either do to the Denisovans. What’s going on here?

This does not necessarily mean that we need to redraw the evolutionary lines among these three groups. This is because of the interbreeding element, which again we already know from prior research was happening all the time among all three species. What likely happened is that at some point after the main split between Neanderthals and Denisovans, Neanderthals acquired a human Y chromosome from interbreeding. What this means is that there was a total replacement of the Neanderthal Y chromosome with a human Y chromosome. How can this happen?

Y chromosomes are unique in that they are inherited only from father to son. This is a more direct lineage than other chromosomal DNA. The only other inheritance that is similar is mitochondrial DNA, which is outside the nucleus in the mitochondrial, and pass only from mothers to daughters. They also pass from mothers to sons, but males don’t pass on their mitochondria so that is always a dead end (with rare exceptions not worth getting into). So Y-chromosomes and mitochondrial DNA have provided geneticists with linear inheritance patterns that are valuable in tracing ancestry of groups. This linear pattern, however, also provides the opportunity for a few lineages to prevail, and even for a single lineage to survive times of very low population (the so-called mitochondrial Eve, for example).

This is what the authors think happened in this case. During a time of low Neanderthal population a human Y chromosome that was in the Neanderthal gene pool from interbreeding with humans became dominant, and in fact ultimately became the only Y chromosome in the Neanderthal population. This could have also resulted from selective pressure, not random chance. A small Neanderthal population would mean lots of inbreeding and accumulation of harmful mutations. This is why even occasional outbreeding is so useful to small populations. The “healthier” Y chromosome from a human could have had a selective advantage over the existing Neanderthal Y chromosome, and came to predominate.

That crossover event would then be the “split” time that the scientists are seeing in the current DNA analysis of Y chromosomes, making it look like humans and Neanderthals have a more recent split than either do with the Denisovans. In short, each aspect of these different hominid populations (modern humans, Neanderthals, and Denisovans) have different lineages all with their own histories – their nuclear DNA, Y chromosomes, mitochondrial DNA, and tool culture. We have to tease apart each separately, understanding that they will not all necessarily line up with each other. And the streams are being crossed all the time, making this more complicated.

But slowly a more and more detailed picture is emerging. We will never get to full resolution likely, given the limitations of fossil evidence, but there is likely a much more clear picture awaiting discovery.