We have 23 pairs of chromosomes. However, all of the other great apes have 24 pairs. So our ancestors - some of whom we shared with those apes - must have had 24 pairs as well. Which means at some point in our evolution there must have been a chromosomal fusion. One pair merged into another, explaining how we "lost" an ape one.
When I say this "must" have happened, this isn't some sort of hypothetical inference. We can see that our second pair of chromosomes is clearly the result of fusion. Right in the middle is where one chromosome "ends" and other "starts". But whilst we know a lot about the product of this fusion, we don't know much else about it. How long ago did it happen? How many individuals had the fusion mutation? Did it offer them any advantage?
Now, the Neanderthals and Denisovans are weighing in on these questions. Genetic data from our closest extinct relatives reveals they also had the fusion. This means it must have happened before the three of us went our separate ways, around 1 million years ago.
And that it might have only happened once in a chromosomal "Adam" we're all descended from.
When was chromosomal fusion?
Pinpointing the moment our ancestors underwent chromosomal fusion is tricky given that we don't have a lot of aDNA for the human family. Most of it comes from the last 50,000 years, when we're clearly modern humans who clearly had a fused chromosome. Beyond that, this data doesn't tell us if the fusion event occurred 500,000 years ago or 5 million years ago.
However, there are some ways around this gap in the data. For that, we have to turn to chemistry.
Your DNA consists of four letters which occur in two pairs. C & G are best buds, as are A & T. But these aren't equal pairs. A & T are joined by only 2 hydrogen bonds which C & G have three keeping them together. The result is the latter have a stronger bond. The result being that - all else being equal - C & G is more likely to replace A & T than the other way round.
Of course, all else is rarely equal so this bias doesn't add up to much. If a shift to C & G breaks a gene then the strength of the bond will count for nothing and that mutation is discarded. So in isolated cases, only 3% of substitutions swap A & T for C & G. Yet over the whole genome, the rates of substitution are basically equal.
However, there are some areas where this bias is allowed to shine through. In particular, where chromosomes "swap" material through recombination. This happens a lot at the ends of the chromosomes, resulting in inflated rates of bases C & G.
Denisovans doing chemistry
Have you followed all of that? Good, because this is where it pays off.
The middle of chromosome 2, where the fusion happened, has that same bias towards C & G. However, it is no longer being excessively recombined as it isn't at the end of a chromosome anymore. Thus, it has slightly less C & G than the tips of the chromosome as it has been exempt from this bias from a little while. In fact, when you calculate it out it's been exempt for about 0.75 million years. Thus the fusion must have happened sometime around 0.75 million years ago.
When you look at the human family tree, this is shortly before the Denisovans split from our lineage. So if the fusion really happened before this, both of us should have it. And we know we do, but what about the Denisovans?
Don't worry, all of that biochemistry you just learnt about isn't useless. The Denisovans fit in with this pattern. Their genome contains a series of repeated bases from where this fusion event occurred. This section can't be extracted from great ape chromosomes, even though they have all the constituent parts in their unfused (and thus unrepeating) form.
Fusion Adam
So we have a fairly decent idea about when this chromosomal fusion occurred. But how many times did it happen? Perhaps it was a repeated event, or there it could have happened just the one time. We might all be descended from a "fusion Adam".
The hypothetical label goes to an "Adam" and not an "Eve" because of bias. Not bias in people (well, not totally because of that) but bias in gorillas. They live in polygamous groups that revolve around a single male. If that male underwent the fusion event it would essentially be instantly spread throughout the entire group. Subsequent interbreeding in the group would soon mean every copy of chromosome 2 was fused.
Evidence for this explanation comes from more than just "the family tree works". All people have the same "fusion" site. This lack of variation suggests it only happened once. When convergent evolution occurs, the effect is the same bu the process can be different. The result is a series of different genes doing the same thing. This is the case for milk
This is the case for milk tolerance, which evolved independently several times around the world. The result is several different milk tolerating genes. Unlike what is seen at the chromosome fusion site.
Conclusion
Our ancestors underwent some chromosomal fusion. Genetic research indicates this happened before humans, Neanderthals and Denisovans split. And it may have only happened once in a "fusion Adam".
A lot of this is based on working back from modern data. Like inferring a family tree based on modern variation. Thus it is vulnerable to ancient data from the time of the fusion. For example, if it turned out there used to be more variation at this site it would challenge the existence of "fusion Adam". Or if there was no variation, it might confirm it. Either way, the evidence is strong, but isn't all in yet.
References
Dreszer, T.R., Wall, G.D., Haussler, D. and Pollard, K.S., 2007. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome research, 17(10), pp.1420-1430.
Fan, S., Hansen, M.E., Lo, Y. and Tishkoff, S.A., 2016. Going global by adapting local: A review of recent human adaptation. Science, 354(6308), pp.54-59.
Meyer, M., Kircher, M., Gansauge, M.T., Li, H., Racimo, F., Mallick, S., Schraiber, J.G., Jay, F., Prüfer, K., De Filippo, C. and Sudmant, P.H., 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science, 338(6104), pp.222-226.
Stankiewicz, P., 2016. One pedigree we all may have come from-did Adam and Eve have the chromosome 2 fusion?. Molecular Cytogenetics, 9(1), p.72.
