Our "Missing" Chromosomes

Maggie Koerth-Baker is a guest blogger on Boing Boing. A freelance science and health journalist, Maggie lives in Minneapolis, brain dumps on Twitter, and writes quite often for mental_floss magazine.

Back in February, I went to the American Association for the Advancement of Science conference in Chicago. The whole thing was pretty much a geeked-out blast, but one of my favorite sessions was this four-hour long symposium, the crux of which can basically be summed up as, "Evolution: It Works, Bitches." This particular tidbit, which I originally heard there in a lecture given by Brown University biology professor Kenneth Miller, is just totally nifty and must be shared.

So here's the thing: We have 46 chromosomes. Our nearest great ape relatives have 48. On the surface, it looks like we must have lost two. But that's actually a huge problem. Made up of organized packs of DNA and proteins, chromosomes don't just up and vanish. In fact, it's doubtful any primate could survive a mutation that simply deleted a pair of chromosomes. That's because chromosomes are to the human body what instruction sheets are to inexpensive, Swedish flat-pack furniture. If you're missing one screw, you can still put that bookcase together pretty easily. But if the how-to guide suddenly jumps from page 1 (take plywood panels out of box--uff da) to page 5 (enjoy bookcäse!), you're likely to end up missing something pretty vital. All this left scientists with a thorny dilemma: How could we have a common ancestor with great apes, but fewer chromosomes?

Turns out: The chromosomes aren't missing at all.
Genetic investigators caught the first whiff of the prodigal chromosomes' scent in 1982. That year, a paper published in the journal Science described a very funny phenomenon. Researchers knew all chromosomes had distinctive signatures; patterns of DNA sequences that can be reliably found in specific spots, including in the center and on the ends. These end-cap sequences are called telomeres. Molecular biologist Elizabeth Blackburn says telomeres are like the little plastic tips that keep your shoelaces from unravelling. They protect the ends of chromosomes and hold things together. Given that important function, you wouldn't expect to find telomeres hanging out on other parts of the chromosome. But that's exactly what the 1982 study reported. Looking at human chromosome 2, the scientists found telomeres snuggled up against the centromere--the central sequence. What's more, these out-of-place human telomeres were strikingly similar to telomeres that can be found, in their proper location, on two great ape chromosomes.

This evidence laid the groundwork for a brilliant discovery. Rather than falling apart, the two missing chromosomes had fused together. Their format changed, but they didn't lose any information, so the mutation wasn't deadly. Instead, scientists now think, the fusion made it difficult for our ancestors to mate with the ancestors of chimpanzees, leading our two species to strike out alone. In the two decades since the original study, more evidence has surfaced backing this up, which leads us to 2005, when the chimpanzee genome was sequenced around the same time that the National Human Genome Research Institute published a detailed survey of human chromosome 2. According to Kenneth Miller, we can now see extra centromeres in chromosome 2 and trace how its genes neatly line up with those on chimpanzee chromosomes 12 and 13. It's a great example of evidence supporting the common descent of man and ape.

I'm currently in the process of putting together a mental_floss story looking at this, and several other awesome experiments revolving around the origins of life. I'm not sure yet when it will be published, but, obviously, I'm really excited about it.

Photo courtesy feverblue


  1. This blew my mind when I first read it and it still does. And imagine that there are still intelligent people who deny evolution. Incredible.

  2. Ummm, so how does that change get propagated? Was the guy/gal who first fused our Adam/Eve? Did fusion occur more than once? Not questioning that it happened, just curious.

  3. I imagine they have to go somewhere after a while, or else the shoelace ends would be scattered everywhere. The number of chromosomes in critters vary all over the place.

    Plants would be ugly to try to parse out.

  4. Am I missing something?

    If two chromosomes fuse into one chromosome, you only lose ONE separate chromosome. So shouldn’t the human count be 47 instead of 45? Or did another pair of chimpanzee chromosomes fuse as well?

  5. @2 : “Was the guy/gal who first fused our Adam/Eve?”

    Not necessarily. At least not if you’re using the “most recent common ancestor” definition. The fusion was probably not the most recent mutation our species has undergone. So that “guy/gal”/ape had lots and lots of descendants and then one of them had another one of the mutations bringing it closer to being a human and it had lots and lots more descendants.

    Also the “eve” wouldn’t even necessarily be the first to undergo whichever is our most recent common mutation, it would be that person’s descendant whose line didn’t die out.

    That was a mess, but it’s kind of difficult to explain / think about…

  6. @4 yes, the fusion occurred in a pair of chromosomes, not a single chromosome. Humans have 23 pairs and apes have 24.

  7. The terminology is confusing because “chromosome” and “pair of chromosomes” are often tossed about interchangeably.

  8. #1 you post could be easily misconstrued as one by an orthodox priest for an evolutionist religion. Fanatical orthodoxy to a theory is the kind of thing that stands in the way of actual science. While it is useful to have a good theory for day to day work to lock yourself into that theory to the exclusion of all other possibilities is as foolish as the church was in the time of Galileo.
    Even the hard math we use only appears to work, to our appearances, but is is not a 100% sure thing, just good enough to allow the technological civilization we now have to work most of the time.
    Just because the opposing argument happens to be mostly right wing or religious is no reason to crawl under a rock.

    This story goes a long way to explaining the problem of a species breaking off and becoming unable to successfully mate with its distant relatives. But it is only one step ion the very long and difficult road to strengthening and testing the current theory of evolution.

  9. Can this post be re-worked to help my layman brain grok it?

    For example, I totally understand what peanut butter is.

    And I also can completely visualize a bar of chocolate.

    Perhaps a “You got your #12 chocolate bar stuck in my #13 peanut butter & now we’re not apes?” metaphor?

  10. For anyone who in intrigued by discussions of this nature, “The Ancestor’s Tale” by Richard Dawkins is a fantastic book. It’s very long, but it covers a huge breadth of the state of evolution, with fascinating examples of all sorts of oddities that have happened along the way. It also discusses why we think we know what we think we know, which is just as interesting to me as the knowledge itself.

  11. Hmmm, is chromosome 2 in humans the first place they looked for mid-chromosome telomeres? They might exist elsewhere, after all.

    Also, some variants of Down Syndrome, instead of trisomy 21, have 2.5 * chromosome 15, which might then be a ‘telomere malfunction’

  12. Book suggestion: Only a Theory by Kenneth R. Miller:


    quick scanned sample from the chapter dealing with the human/chimp chromosome issue:


    The book has much more Great Stuff in it.

    At first, I was thinking that the chromosome chapter was in Your Inner Fish, and was about to recommend that. Of course, it isn’t in there, but I’m recommending it anyway.


  13. “That’s because chromosomes are to the human body what instruction sheets are to inexpensive, Swedish flat-pack furniture. If you’re missing one screw, you can still put that bookcase together pretty easily.”
    Love that.

  14. @12
    Think of these as books for cooking up proteins. Your book count is down one. Then you find “one book” that had a back and front cover in the MIDDLE.

  15. How big a role does the enormous amount of redundancy in the genetic sequence enable this kind of thing? Or the fact that a huge amount of the genes we carry are never expressed in any way?

    And, anyway, how remarkable is this? After all, ostensibly all life descends from a single common ancestor, but 46 or 48 chromosomes are by no means the only possible options. This kind of thing, or another mechanism with the same or opposite result, has happened many many times.

    @#8: What part of the evolutionary theory do you have a problem with? Virtually all human knowledge is imperfect, but some ideas have more and disparate evidence pointing to the same conclusion. Evolution is one of those ideas — a ton of evidence from different fields all seems to be pointing to the same conclusion.

    Just because I didn’t actually personally witness the Holocaust, but yet believe that it happened based on evidence from people whose knowledge on the issue I trust, doesn’t make me a religious Holocaust Believer, swearing fidelity to the god of Holocaust existence. There has to be a threshhold.

    Belief that evolution happened isn’t a religious beief, and they aren’t equivalent by any means. Evolution would be easy to disprove — a rabbit fossil found in Carboniferous strata would do the trick. Religious belief is unswaying in the face of evidence. Science, when it works correctly, is not.

  16. This is truly a facinating article! But, what troubles me is that the mutation usually occurs through reproduction. And so, if the mutation happened, it would have happened at a single instance- otherwise some sort of widespread genetic mutation (the likes of which seen in an X Men movie) would have to take place. Since X Men movie plots aren’t accepted in the canon of evolution literature, chances are said mutation had to occur during reproduction. And of this mutation happened during reproduction, it would mean that the offspring would be unable to reproduce with any other offspring, by definition of the mutation which makes it impossible for humans to mate with monkeys. Given the frequency in which this mutation would have to happen, so that the new species of animal would have to survive (that it may reproduce with other members of the same species), one would imagine that this slight genetic mutation would be repeately observed in the offspring of modern day chimpanzees.

    One could argue the continual ‘missing link’ argument, that the monkey had a mutant offspring, which still could reproduce with the original monkey. This ideology is similar to simple punnett square genetics: that the ‘human mutation’ is a heterogenus mutation of the genes. Similar to how the color of flowers, or even the way our hair is, is determined. If one accepts the theory of the ‘missing link’, with DNA that could mate with chimps and would also facilitate evolution into human beings as we know them today, one could argue that this mutant possesses a DNA that is unstable, which would cause the fetus to abort. What I would suggest is that if we are dealing with a mutant missing link, since the missing link isn’t living among us today, it is a sign that the proposed theoretical DNA is too unstable to exist. This instability is evidenced by the fact that after the first evolution it immediately evolved into something resembling humanity. Stability would be needed because evolution, which we are taught, takes thousands upon thousands of years to happen. Since we cannot find a living representation of the species that was stable enough to produce Homo sapiens- a living intermediate missing link (which isn’t too much to ask since Chimps exist), it is not folly to continue to believe in the merits of creationism. This living missing link would be proof that our genetic ancestor was capable enough to survive long enough to permit evolution. Unless you chose to believe that God killed them all off to hide the truth regarding evolution. Thank you for your time.

  17. @#17 it doesn’t matter what #8 has problems with specifically, he’s still right. Always question, always think. Don’t accept blindly. Examine and explore. Without that, you are treating it like a faith. There are always more questions to be asked and more answers to be found. Don’t be so defensive about people questioning things. In science, it’s a Good Thingâ„¢.

    For example, a couple of questions I have on this is: assume that the chromosome fusion occured to one individual. How did it get passed on? Wouldn’t it have precluded mating with those who didn’t have the fusion occur? Why did that fusion become dominant in the offspring of that one individual when it was surrounded by the unfused neighbours? If someone can answer these, then my understanding is increased. If not, then maybe it’s something that needs to be looked into more.

  18. Thanks for feeding my chromosome geekery. It makes me very curious about where this discovery might lead. As someone mentioned above, animals and plants have all kinds of different numbers of chromosomes–from a single pair all the way up to 1200+ for one species of fern, and there are no obvious patterns. It would be fascinating to look at the current classification of species and append chromosome number. Did species tend to evolve by fusion or by fission of chromosomes?

    #14 – The chromosome 15 disorder you describe (if it’s the one I’m thinking of) is not actually a variant of Down’s, although some of the symptoms are similar and there is “extra” genetic material just as there is in Down’s. I’ve also always found it interesting that besides trisomies of the sex chromosomes, there are only two other trisomies besides Down’s that are at all survivable in their complete form–trisomies 13 and 18–and those only just barely.

  19. I realise that chimps have moved on since we shared a common ancestor but I wonder (ethics aside) what the result would be if we fused these two chromosomes together in a chimp gamete?

    I don’t even know if this is possible with current technology but it would be interesting to see what changes would occur in the new chimp offspring and whether they would be able to continue to breed with other, non-fused chimps.

  20. I’m putting “Evolution: It Works, Bitches” on a t-shirt and wearing to church. Awesomely put.

  21. Thank you for posting this, Maggie!

    I teach biology to kids, among other things. This is very useful. Keep it coming.

    BTW, I grew up in Cobb County, Georgia, USA, where as recently as five years ago, the school board was putting stickers on all of the Biology textbooks dismissing evolution by natural selection as “a theory, not fact:”


    Which it is, from a purist’s point of view, but they never went on to emphasize how important theories have been in a historical context.

    Stuff like this helps push back the umbrella of ignorance for kids who get tired of the bullshit of ages past and long for reviewable data.

  22. I imagine a creationist saying “centromeres and telomeres. . . you just made those up, didn’t you!?”

  23. @FAC33,

    Don’t forget XXX, (not PORN) or XYY (happens, probably not pathological)

    Personally, I’ve always been intrigued by the relatively-same-sized chromosomes, except for poor stunted Y!

  24. Wow, this is super neat.

    Another way to look at this:
    # cat ch12 ch13 > ch2

    It is not mentioned in the article, but chromosomes are numbered in decreasing order of size. So, chromosome 2 is the second largest human chromosome. The fact that it is actually two chromosomes in one explains its size.

    I wonder if deer (or was it horses) with their 4 chromosomes show this concatonation.

    @#20 Since the mutation involved chimp chromosomes 12 and 13 sticking together end to end, it’s not really a problem of extra or missing dna when the mutation happened. There may well have been differences in how certain genes were up or down regulated because of the superstructure differences between the individual chromosomes and the cojoined version. Now however, we humans have probably seen changes in what is now chromosome 2 so that it has become a real one way gate.

    We really don’t know how much funny business happens in our DNA stream on an individual basis because we have sampled only a very small subset of the populace’s DNA. There are many chimeras among us (people with two sets of genotypes mixed in their body). Who knows how many chromosome concats produce viable pregnancies that end up not propagating because the concat “broke” when going through meosis in the child. Who knows. BUT with the ability to quickly sequence dna from an individual within the next few years – we may find more oddities that we didn’t think should exist.

    Fun stuff.

  25. “Rather than falling apart, the two missing chromosomes had fused together. Their format changed, but they didn’t lose any information…
    That sounds like highly advanced alien genetic engineering. Von Daniken was was right!

  26. @21 it is much more likely that the original mutation was a lot different. For example maybe the chromosomes weren’t completely fused or they could fuse and unfuse or something similar for MANY generations before it became permanent and interbreeding was impossible. That’s probably not exactly what happened of course, but something similar. Meaning, for a long time the people/animals with the new mutations could interbreed. Otherwise it would be impossible.

    What we do know now is that it is likely that it did happen. So we just have to figure out how.

  27. And the week right after they will all wear a T saying: “Evolution: it works for bitches.”

    Can’t win with them: they’ve evolved that way. I wish that I could see the day we become two different species though.

  28. < <...the fusion made it difficult for our ancestors to mate with the ancestors of chimpanzees...>>

    “Difficult” but not impossible? Does this revelation mean chumans may be possible? (Please say yes.)

  29. I’m just a layman, but I’m not sure that it’s an out-and-out law that creatures with unmatched chromosomes can’t produce fertile offspring. More of a guideline that scientists have surmised from observing the natural world.

    We know, for example, that donkeys have a different number of chromosomes from horses, yet a mating between the two produces mules, with an odd un-paired chromosome. So we know that a simple unpaired chromosome doesn’t cause any problems in the resulting organism. The problem comes when that offspring tries to reproduce, I’m guessing at the recombination phase, the unpaired chromosome having nothing to recombine with.

    However, I wonder if the recombination might work if, say, one parent has the mashed-up chromosome and the other has the two chromosomes still separate when the two parents still have all the genetic sequences on the relevent chromosomes in the same (or very similar) order. When it comes time for their offspring to reproduce, when his or her genes do the recombination thing, the mash-up chromosome from one parent might still manage to combine with the separate chromosomes from the other, especially if the two parents are related. I guess that would produce some gametes with a mash-up chromosome and some with the separates.

    So the mash-up would spread through the population as long as it could combine with similar separate chromosomes. But if the chromosomes were too dissimilar (due to mutation) then sterile offspring would result. But by the time that becomes a problem, there would be enough mash-ups in the population to breed with each other and thereafter form a separate population.

    But I’m just guessing.

  30. That hairless creature has to be one of my sole mates. I am like that a lot. Biological computers in simplest form show up as Prions. A more advanced computer works in single cell beings. Single cell beings of one sort breath oxygen. Took some time but they got smart enough to build us. If they just had the presence to predict the future I’m sure they wouldn’t have bothered to waste the technology. Brains cannot discover themselves. Keep trying tho.. it is fun to watch your hair fall off.

  31. #30 – nothing – not a thing – appearing on that website has anything to do facts, science, reality. Did you even read the stream of nonsense you pointed to? I’m still trying to bleach my eyes after looking at it.

  32. This very issue is covered very thoroughly and in a very-easy-to-understand way by Daniel Fairbanks in his book “Relics of Eden: The Powerful Evidence of Evolution in Human DNA” :


    It has it’s own chapter (“Fusion”, chapter 1), some of which you can even read on the above link using the “Search inside this book” link. Maggie if you are interested in writing about this topic you really have to read that chapter, it’s probably the best explanation you’ll get anywhere (it even has lots of figures to accompany the text).

  33. I first heard about human chromosome two about 3 years ago when I read what Ken Miller said about it at the Dover trial. I was shocked. I had no idea scientific evidence could be this powerful. I thought this settles it. If creationists are told about this evidence they couldn’t possibly continue being creationists. I was wrong. It turns out that creationists are way more stupid than I thought possible. — bobxxxx

  34. Stunning science, but although it adds still more evidence of common ancestry onto the already large pile, that alone will never convince those, with an emotional stake in denial, that they are wrong. For every piece of evidence, there is a credentialed “expert” willing to speak up on the biblical literalist’s behalf (see anonymous at 30 above for an example) and at that point, your evolutionary unbeliever may choose which plausible story to disbelieve, mostly unencumbered by the sort of education that would throw light upon the differences in their arguments. The egoboost these “experts” receive in return more than explains their own self-deception.

  35. I’m sorry (polite mode sorry),but whenever I read a creationist screed that “refutes” evolutionary theory I find the fundamental disconnect so vast in their lack of any logical continuity I cannot even finish reading. They are gits. Just gits.

  36. There are many such screeds, of varying levels of sophistication, as well as varying levels of regurgitation stimulation…

  37. Kenneth Miller is also awesome, imo, because he’s Catholic, like me, and sees no reason why evolution contradicts religion or faith in God, like me, and thinks creationists are incredibly foolish, like me. And unlike me, he’s a brilliant biologist, so there’s where the awesome comes in.

    He’s got another book called Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution, for those who are interested. A good antidote to Behe.

  38. #30’s link above does have one good point, however:

    Trying to prove a current species is a modification of another current species is not a valid argument for a common ancestor.

  39. @ #49:

    I’m not religious, but I see many, many reasons why evolution might be taken to contradict religion and (albeit to a slightly lesser extent) faith in God. Just depends on what your religion is really, doesn’t it?

  40. Interesting article, even without the shock of seeing my photograph as an illustration! Thanks for the credit. Strangely, I took that photo a couple years back at the Albuquerque zoo in the company of my cousin and her husband, who happens to also be named Kenneth Miller.

  41. I’m not a bio scientist, so this is mere hypothesis, but I think a lot of people are missing 1 thing, and its implication.

    This mutation, like down syndrome, isn’t just an isolated event. Part of our genetics is the propensity to have this sort of mutation – it wasn’t just some cosmic ray that did it one time only. In particular, this isn’t just a normal old genetic mutation in the code, this is a mechanical error, and probably had a small percentage chance of occurring occasionally in a large subset of the population.

    And especially in a large community of social, nurturing apes, they probably had a small but significant population of members with the same mutation. Most likely we didn’t have an Adam and Eve pair of apes (which wouldn’t be much genetic diversity to start with anyway), but an initial population of several hundred, over many many years as the normal ape population continued to have the rare mutated offspring that would join the gene pool of the new offshoot group living amongst them.

  42. #49 & #52 – since pretty much all religions claim that their god/gods/spirits/whatever created the world (pretty much) as it is now – and usually in a miserably short timeframe and usually without reference to the staggering number of stars and galaxies, let alone simple stuff like, oh a spherical planet orbiting the sun – then every bit of science that establishes the lack of validity of those claims pretty much destroys said religion. And since those gods are nothing more than the inventions of the promulgators of the religions in question, we can pretty much discount them as having any actual existence.

  43. Anonymous “I would like to direct your attention to an article written by a genetic scientist relating to this:”
    Well “Anonymous” (if that is, in fact, your real name), “Answersingenesis” and “scientist” are pretty much mutually exclusive terms. A Venn diagram, in other words, would show very little overlap.
    With scientists of the methodological naturalist type evidence leads to a (tentative) conclusion, while “scientists” of the capital C Creationist type the evidence is interpreted based on the (absolute) conclusion.
    Also, read Your Inner Fish, Making of the Fittest, Endless Forms Most Beautiful & Relics of Eden.

  44. Umm, they are called aglets. the plastic things that hold your shoelaces together. Aglets. Just thought you all should know.

  45. @#56 Tim, science can refute the simple literalist interpretations of religion, and all are better off for it. OTOH, the Golden Rule seems a good way to enourage the social development of an animal evolved to rely on learned behaviors. Think baby and bathwater.

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