The history of humanity, as we've read it through DNA, has been written largely by females. Mitochondrial DNA, which is inherited only from our mothers, is short and easy to sequence, so researchers have frequently relied on it to study human DNA, both in present populations and in old bones.

But as DNA sequencing technology has improved, it has become progressively easier to sequence all the DNA that an individual carries. If said individual is a male, the resulting sequence will include the Y chromosome, which is inherited only from fathers. With more data in hand, researchers have been able to perform an analysis of the Y chromosome's history, and they've found that its sequence retains the imprint of both the migrations and technological innovations that have featured in humanity's past.

How to read a Y

Most chromosomes in the cell are present as two copies, which allows them to swap genetic material. Over time, this swapping will mix up the mutations that occur on the chromosome, making their history difficult to untangle.

The Y chromosome is different in that males only have a single copy, and most of it doesn't undergo any genetic shuffling (a small region can recombine with the X chromosome). As a result, any mutations that occur on a single Y chromosome will always be inherited together. This makes the Y great for reconstructing history.

Let's say that, deep in our past, a mutation we call A occurred and gradually expanded in the population. Later, one of the descendants who carried A experienced a second mutation, B, which also expanded a bit. If we sequenced a population of 100 today, we might see 50 people who carry A and 30 who carry B. But every single person with B would also carry A. This idea allows us to infer the order in which these changes occurred and, given the average rate at which mutations appear, their timing.

Now, layer a bit of history on top of that. If A occurred after humans migrated out of Africa, it might be widespread in populations elsewhere around the globe. But if B occurred later, after further migrations, it might only show up in a specific region—say, Australia. So we can not only learn about the timing of different mutations, we can often figure out where they must have occurred.

But wait, there's more. If a population is relatively steady, there won't be much change in the number of mutations—for each new one that appears, another is likely to die out. But when a population is expanding, new mutations are more likely to be retained and show up in modern lineages. When making a Y chromosome family tree, this process will appear as a sudden burst of branches in a short amount of time.

Y history

To read this history of the Y, a large team of researchers took advantage of the sequences generated by the 1,000 genomes project, which has now gone well past its initial goal of completing 1,000 human genomes. The researchers found 1,244 genomes with a Y in the database and were able to identify more than 60,000 individual base differences they could track. These differences were subjected to the sorts of analysis described above.

First, the researchers found that the common Y ancestor dates to 200,000 years ago—much earlier than the most likely time of the last female common ancestor. The last non-African common ancestor dates to 75,000 years ago, shortly before the migration out of Africa is thought to have occurred. There was also a large boom in population, with many new lineages appearing about 50,000 years ago, when humanity's global migration was in full swing.

One oddity here is that the most common lineage in Africa didn't start there; it likely originated in the Middle East and was taken back to Africa by counter-migration. The Y chromosome data also suggests that humans first migrated along the southern coast of Asia to Southeast Asia and then spread from there to populate areas as distant as Europe and the Americas.

The authors identified times and places where the Y chromosome saw many new lineages arise, a sign of rapid population expansion. These instances of new lineages were numerous and rather excessive. "Such extreme expansions are seldom seen in the [mitochondrial] DNA phylogeny," the authors note, before going on to argue that as "the [lineage] expansions we report are among the most extreme yet observed in humans, we think it more likely than not that such events correspond to historical processes that have also left archaeological footprints.

What are those historical processes? One is the arrival of humans in the Americas, which appears to have occurred about 15,000 years ago—consistent with the archeological evidence. Another big expansion occurred just prior to the Bantu expansion in Africa, a large internal migration that spread across much of the continent.

Other expansions occurred just prior to the onset of the Indus Valley civilization, and two occurred in Europe associated with the migration of people in from the Asian steppes and the development of a new technological culture about 4,800 years ago. The big exception to this pattern? "East Asia stands out from the rest of the Old World for its paucity of sudden expansions," the authors write, "perhaps reflecting a larger starting population or the coexistence of multiple prehistoric cultures wherein one lineage could rarely dominate."

Overall, the picture drawn from the Y chromosome is consistent with things we knew about from archeology, and it's broadly consistent with the picture we've derived from studying female lineages. But because male lineages can expand much faster, the Y provides some extra details about some of the more turbulent moments in humanity's past.

Nature Genetics, 2016. DOI: 10.1038/ng.3559 (About DOIs).

Listing image by MIT