Human history traced via the Y chromosome

Male lineages expand rapidly at key points in our past.

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, soresearchers have frequently relied on it to study human DNA, both in present populations and in oldbones.

But as DNA sequencing technology has improved, it has become progressively easier to sequence allthe DNA that an individual carries. If said individual is a male, the resulting sequence will include the Ychromosome, which is inherited only from fathers. With more data in hand, researchers have been ableto perform an analysis of the Y chromosome’s history, and they’ve found that its sequence retains theimprint 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 historydifficult to untangle.

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

Let’s say that, deep in our past, a mutation we call A occurred and gradually expanded in thepopulation. Later, one of the descendants who carried A experienced a second mutation, B, which alsoexpanded a bit. If we sequenced a population of 100 today, we might see 50 people who carry A and30 who carry B. But every single person with B would also carry A. This idea allows us to infer the orderin 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 bewidespread 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 ofdifferent 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 ofmutations—for each new one that appears, another is likely to die out. But when a population isexpanding, new mutations are more likely to be retained and show up in modern lineages. Whenmaking a Y chromosome family tree, this process will appear as a sudden burst of branches in a shortamount of time.

Y history

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

First, the researchers found that the common Y ancestor dates to 200,000 years ago—much earlierthan the most likely time of the last female common ancestor. The last non-African common ancestordates to 75,000 years ago, shortly before the migration out of Africa is thought to have occurred. Therewas also a large boom in population, with many new lineages appearing about 50,000 years ago, whenhumanity’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 theMiddle East and was taken back to Africa by counter-migration. The Y chromosome data also suggeststhat humans first migrated along the southern coast of Asia to Southeast Asia and then spread fromthere 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 signof 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 yetobserved in humans, we think it more likely than not that such events correspond to historicalprocesses that have also left archaeological footprints.

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

Other expansions occurred just prior to the onset of the Indus Valley civilization, and two occurred inEurope associated with the migration of people in from the Asian steppes and the development of anew technological culture about 4,800 years ago. The big exception to this pattern? “East Asia standsout from the rest of the Old World for its paucity of sudden expansions,” the authors write, “perhapsreflecting a larger starting population or the coexistence of multiple prehistoric cultures wherein onelineage could rarely dominate.”

Overall, the picture drawn from the Y chromosome is consistent with things we knew about fromarcheology, 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 ofthe more turbulent moments in humanity’s past.

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