The secret history of X and Z – how sex chromosomes from humans and chickens found common ground

By Ed Yong | July 11, 2010 1:00 pm

XY

In humans, two chromosomes – X and Y – determine whether we are male or female. Of the two, Y tends to get more attention because of its small, degenerate size. Both X and Y probably evolved from a pair of ordinary chromosomes that have nothing to do with sex (also known as autosomes). The story goes that one of these autosomes developed a gene that immediately caused its bearer to become male, and eventually became the Y chromosome of today. The other one became X.

Throughout its history, Y has been a hotbed of genetic change, gaining, losing and remodelling its genes at breakneck pace, and shrinking by 97%. Its partner – X – has allegedly had a less eventful past, and should faithfully represent the ancestral autosome. This history of X and Y was first proposed in 1914 by Herman Muller, and ever since, his assumptions about X’s stability have gone untested. Now, it seems that Muller was wrong. Daniel Bellott from the Howard Hughes Medical Institute had uncovered the secret history of X, which turns out to be no less storied than Y’s tale.

Bellott’s work began, surprisingly, with chickens. Birds also have sex-setting chromosomes, known as Z and W, which vary between the males and females. The big difference is that in birds, males are ZZ and females are ZW – obviously in humans, males are the ones with the differing pair. Like the Y chromosome, W has shrunk and changed considerably while, as Bellott says, “the sex chromosomes that are present in both sexes (X and Z) were supposed to be above the fray”.

But Bellott showed that this isn’t true by completely sequencing the Z chromosome for the first time. (The chicken genome has been published before but sex chromosomes are notoriously difficult to sequence). His draft revealed that both X and Z arose from different autosome ancestors, and none of the 1,000 genes on the Z chromosome has a counterpart on the X. Nonetheless, they have independently evolved very similar features.

Both are very loosely packed with genes. In any given stretch of DNA, the Z and X chromosomes have half as many genes as other autosomes do. And among these patchily distributed genes are piles of litter – long stretches of repetitive DNA with no clear function. Most of these are sequences known as LINEs. “These LINEs are basically selfish elements,” says Bellott. “If a cell is like a computer, the genome is like a hard drive, and the LINEs are computer viruses that copy themselves over and over, filling up the drive.” Z has 70% more LINEs than any other chicken autosome.

The LINEs can’t quite account for all the extra space between the genes, but that might just be because they’ve decayed over time. Bellott explains, “We think that, for whatever reason, the mechanisms for cleaning out this “junk DNA” are less effective on Z and X chromosomes than on autosomes. As a result, junk builds up in between the genes on the Z and X, but because it doesn’t really do anything for the organism, it slowly decays. After a while, we can’t even recognize the “junk” as LINEs anymore. After millions of years as sex chromosomes, it just looks like the X and the Z have a low gene density.”

Why the similarities? It’s possible that both X and Z evolved from autosomes with features that made them more likely to become sex chromosomes. Perhaps, for example, their genes were already sparsely distributed. But Bellott ruled out this idea. He compared X to its closest counterpart in chicken, and Z to its equivalents in humans – none of these relatives had any structural features that made them stand out among other autosomes. There’s nothing that singles them out as ideal candidates for the role of sex chromosome.

So it seems that X and Z chromosomes are true examples of convergent evolution – when two entities take different evolutionary roads to arrive at the same adaptive destinations. Not only have their genes become more widely spread apart, they have also gained extra ones. While the tiny Y and W chromosomes have jettisoned genes at great speed, X and Z seem to have gained genes since their ancient days as autosomes.

The identity of these added genes is particularly surprising – they’re mostly male-specific genes that are only switched on in the testes. And there are lots of them, arrayed in a huge block. These testes-genes make up around a sixty of the Z chromosome and 1% of the chicken’s entire genome!

Z_chromosome

This is particularly surprising because the Z chromosome is present twice in male birds, but the X chromosome is only present once in male humans. You might have expected, for example, the X chromosome to be richer in female-specific genes. Bellott says, “The convergent specialization for testis function suggests that there are strong evolutionary pressures on male reproduction.” Indeed, other studies have suggested that traits related to male reproduction are some of the fastest evolving characteristics in the animal kingdom. These pressures are strong enough to trump any difference in the XY and ZW sex-setting systems.

Reference: Nature http://dx.doi.org/10.1038/nature09172

More on sex chromosomes:

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Comments (11)

  1. I don’t know why a lack of Z/X homology between birds and mammals is surprising. Chromosome number is so plastic over time, and recombination so dynamic, that it should be obvious chromosomes are merely ephemeral associations of DNA. I’d find the converse a much more shocking discovery.

    There’s an Australian ant genus, Myrmecia, where chromosome number varies from N=1 (all genes on a single massive chromosome) to N=50.

  2. excellent review! though yes, i second alex’s response. though i’m not too up on chromosome evolution, so it’s an impression only.

  3. Tk

    [“sixty” -> “sixth”?]

    The abundance of male-specific genes on the X chromosome (as opposed to any of the autosomes) seems to require some explanation. Is there a simple mathematical reason such genes maximize their impact by being on the X chromosome? I suppose I could ask the same question about the Z chromosome in birds, too.

  4. @Alex and Razib

    The lack of Z/X homology isn’t a huge surprise, but their orthology has been a long-standing hypothesis in the field of sex chromosome evolution. Susumu Ohno (who literally wrote the book on vertebrate sex chromosome evolution) predicted that the Z and X would be orthologous back in 1967, albeit on the basis of very limited data.

    In any event, it was logically necessary to demonstrate their independence before exploring convergence.

    @Tk

    There’s actually an elegant mathematical treatment of why sex chromosomes should accumulate genes for traits of greater advantage to one sex than the other (sexually antagonistic traits) . See this article by William Rice: http://www.lifesci.ucsb.edu/eemb/faculty/rice/publications/pdf/07.pdf

    Note that this applies to the accumulation of female advantage genes as well as male advantage genes, on both the X and the Z chromosomes.

    Thank you all for your interest!

  5. Tk

    Thanks, Dr. Bellott. This is exactly what I hoped for. So (says Rice’s model) recessive male-favoring alleles and dominant female-favouring alleles enjoy a head start if they live on the X chromosome. How elegant! I love applied math(s).

  6. And now for something completely different: apparently you write like Stephen King. http://iwl.me/b/b3a26720. Hey, it could be worse: I apparently write like Chuck Palahniuk. And that’s when I’m trying to sound smart….

    Also: the test is bollocks.

  7. Rich

    Michael Meadon:

    “Also: the test is bollocks” should be, “Also: the testes are bollocks”.

  8. Richard L

    Ok, I didn’t really understand much of this. Mostly because I never really use biology-talk and I’m getting tired reading the last paragraph over and over.

    Is the conclusion that an under-represented sex-chromosome is harder pressed for adaptations than the majority sex-chromosome? If so, is it because (or implied by the study/any study that) the sex with odd chromosomes have a harder time ‘transmitting’ a specific chromosome than the paired same-chromosome sex has to ‘transmit’ one of their (more akin) chromosomes? As I see it, a case of one of three chromosomes having a higher survivability chance per default than the one alone chromosome?

    I’m also interested to know, since my biology is so very poor, if it is known whether the same-chromosomes mix their genomes somewhat during sex-cell-division? I’ve heard about this in other chromosomes, I don’t know any real data though.

    I am sorry for my poor understanding of terminology in biology and hope that my questions get through.

  9. Eleanor

    Hi Richard,

    It is an amazingly complex topic.

    The surprising bit in the final paragraphs is that, whether males are coded XY or ZZ, the ‘big’ sex chromosome in the system is stuffed with male determining genes, regardless of anything else. (You are right that one of the chromosomes (i.e. Y or W) will be present in a population at a 1:3 ratio to the other (i.e. Z or X), but that is a whole new can of worms….)

    The X chromosomes do cross over and recombine but obviously only where it is XX. The Y chromosome is a little odd, in that (in humans) a tiny section does recombine with the X while the rest never mixes. This bit is called the ‘non-recombining Y’.

  10. Sven DiMilo

    Sex chromosomes are certainly independently evolved in birds and mammals; both likely had ancestors with temperature sex determination (as in all modern crocodilians and almost all turtles, plus some lizards).
    Male-specific genes on the mammalian X would ensure a consistent gene dosage. It’s never expressed heterozygously.

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