Gene survival and death on the human Y chromosome

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I opened my mailbox last week, and what should appear before my wondering eyes, but the new issue of Molecular Biology and Evolution. Inside is our recent (and open access!!) paper: Gene survival and evolution on the human Y chromosome. Here’s my summary of our work. (Editorial Note: it is so, so much easier to distill down research articles that I haven’t spent years of my life on.)


In humans, genetic females have two X chromosomes and genetic males have one X chromosome and one Y chromosome:



You might have noticed from the cartoon above that the human Y is much smaller than the human X. But, it wasn’t always this way. Ancestrally, the human X and Y were the same size, and had the same genes. Over time, however, the Y has shrunk, but both the X and Y have also gained some genes. To better understand how the X and Y became so different, and how the evolution of the two sex chromosomes are correlated, we asked three main questions:

1. What has been lost from the Y?
To know which genes were lost, we first had to identify which genes were on the ancestral sex chromosome pair. By comparing the genes on the human X with the genes the X in other species, we identified a set of genes that were likely on the ancestral X chromosome: 600 in total. Then, by searching the Y chromosome for the relics of all of these genes, we identified three classes of sex-linked genes. We should think of each of the 600 ancestral genes as a pair (with one copy on the X, and one on the Y). All of these pairs have a working copy on the human X. Some pairs have a working (functional) copy on the Y, some have a broken copy on the Y (degraded), and some are missing their Y-copy.

Many genes have been lost from the ancestral Y, but a few persist.


So, while some Y-linked genes have survived (I have another paper discussing this), and there have been some unique additions to the Y chromosome, we can see that the Y has lost functional capabilities for 96.83% of the genes that it once shared with the X. Wow!

2. Are there indicators of whether a Y-linked gene will be retained?
We can learn about the evolution of the sex chromosomes by studying differences between classes of sex-linked genes defined above. Specifically we asked, do features of X-linked genes suggest whether their Y-linked partner are retained or lost? In some cases, yes, they do.

First, we found that human X-linked genes with very few changes across mammals were more likely to have a working Y copy. So, if a gene is important enough to survive over long evolutionary time in roughly the same condition across very different species, then it might be very useful to the organism, so it would be important to have that gene in a working form in both males and females in the same species (human).

Second, we looked at expression. Genes can sometimes be “on” (which we would call expressed) or “off” (not expressed), but more often they can fall within a range. It’s like a light with a dimmer switch. The light can be turned on very brightly, but can also dimmed to a very low level without being “off”.  We found that X-linked genes that were highly expressed (bright) were more likely to have a working Y copy. This might mean that, for these genes, the level of “brightness” or expression is important, so that it is highly beneficial for these genes to be working very hard in both females and in males.

3. Does gene loss on the Y affect the evolution the X?

Okay, so some features of the X-linked partner might predict whether it’s Y-linked partner will survive, but is there any feedback from the Y back to the X chromosome? Yes!

Let’s think back to that first picture: females have two “big” X chromosomes, while males have one “big” X and one “little” Y. And, I’ve shown you that the Y chromosome has lost (either because of broken copies, or completely lost) almost 97% of the genes that it once shared with the X. This might lead you to believe that there are more genes expressed in females than in males. But, in many mammals, females silence most of the genes on one of their X chromosomes (X-inactivation), to equalize the dosage of genes expressed between males and females.



Although it has been hypothesized, we showed that the pattern of genes subject to silencing in females among the three classes above is consistent with a process whereby silencing evolves in response to gene loss on the Y chromosome. Moreover, this pattern suggests that some amount of time must pass to allow the signal (that the Y-linked partner is no longer working) to reach the X-chromosome before silencing can occur.

The paper is open access, so if you are curious, you can read it here.


Mol Biol Evol. 2013 Apr;30(4):781-7. doi: 10.1093/molbev/mss267. Epub 2012 Dec 4.

Gene survival and death on the human Y chromosome.

Source


41 Comments

But what about the appearance of design?

Oh right, it’s missing.

Glen Davidson

Thanks for the link. Looks like a very interesting paper. Of course the pattern observed is exactly what you would expect if the process of evolution had acted to shape the human XY system over millions of years. And it’s also another example of how duplicated genes can diverge to take on new functions.

Yes! I have a 2009 paper (that I may be inspired to blog about) where we investigate X and Y evolution by using this exact concept - where X and Y gametologs can be viewed as duplicated genes, after recombination suppression. Well, in males.

But in birds the other way around than it is in mammals?

But in birds it’s the other way around than it is in mammals?

Rats, I thought the first one didn’t go through!

“the pattern of genes subject to silencing in females among the three classes above is consistent with a process whereby silencing evolves in response to gene loss on the Y chromosome.

Okay, you lost me. If gene g were on both X and Y, and some silencing of g were advantageous, how would you tell if loss in females were a response to a loss on the Y chromosome, and not some other kind of selection?

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https://me.yahoo.com/a/gAuc5roo0P8P[…]xCia4-#a0545 said:

Let’s get one thing straight about Darwinism. If NS acting on RM explained anything then it would explain how one protein evolves into another. I challenge you to name me just one father protein, then name its two child proteins which are more than 20 amino acides different then inform me how NS acting on RM forced that change from the father protein into the two child proteins. There are about a billion to a trillion different proteins existing on Earth and Darwin’s wonderful theory has not explained how any protein more than 20 amino acids different from its sibling protein evolved due to NS. And several proteins are more than 1000 amino acids long, some of them even 27,000 amino acids long. This theory hasn’t explained anything and somehow it managed to become orthodoxy.

http://en.wikipedia.org/wiki/Moving_the_goalposts

GET OUT OF HERE!

Not until he’s done his 10 posts for credit.

Sorry to interrupt this valid discussion of a scientific topic, but I’d just like to make the underwhelming announcement that this is my last comment on PT.

Not because of this thread, of course.

People who want bad things often try to justify those desires. Frequently, they use religious claims to make those justifications.

But there is a history of people distorting science, and then making the claim that inhumane social policy is justified by or somehow “compatible with” science.

Such claims are nonsensical. Science tells us how the physical world works. It does not tell us what we “should” do.

I’ve frequently pointed out that obvious fact that organized efforts to insert evolution denial into public school science class, in the US, currently emanate from the political right. I have pointed that out because it’s true, and to combat such organized efforts, one has to understand them.

If they emanated from the Green Party I’d make the same observation, but, although the Green Party has a somewhat mixed record in terms of support for valid science (ranging from excellent to dismal, depending on the issue), there is no significant connection between the Green Party and organized political creationism.

What I would not do is to claim that my particular subjective ethical values and preferred political ideology are obliged or favored by science.

When people claim, explicitly or implicitly, that science in some way obliges a particular political or economic ideology, they damage their own credibility, the credibility of those who voluntarily associate with them, and potentially, the public credibility of science.

And quite bluntly, if they make the claim that an extreme, inhumane, and unpopular ideology is especially “scientific”, they do even more damage, than if they had made the claim that a more mainstream ideology is such. The logic error is identical but the emotional impact is stronger.

Another good way to undermine the credibility of a forum, and by extension, that which is associated with it, is to block feedback with mechanisms like comment blocking or “invitation” requirements. These are the instincts of a narrow, authoritarian, rigid, juvenile, over-privileged, and insecure mentality. For example, they are strongly associated with William Dembski and his successors as moderator of UD.

An even better way to undermine credibility is to promote an ideology that is absurdly at odds with the ostensible purpose of the forum. For example, a forum ostensibly concerned with science education in public schools, giving preferential posting privileges to someone who adheres to an ideology that opposes public education altogether.

I am not someone who is known for an inability to tolerate the views of others; on the contrary, I am mainly known for being perhaps excessively patient with eccentric or extreme views.

Therefore, when I say that sticking bull$hit posts by Timothy Sandefeur, which promote “libertarianism” using the time-dishonered mechanism of implying that “science” supports some particular ideology, with blocked comments, as prominently in the headline position as say, this excellent discussion of sex chromosomes, damages the credibility of this venue, I hope someone takes it seriously.

They squat there for days at the top, and that’s what anyone who views this site during those days sees first.

If his conscious or unconscious objective is to drive away moderate, mainstream progressive science supporters, he has succeeded again. I’ve had it. And I don’t think I’m the first.

In the unlikely event that anyone gives a damn, they can contact me by email.

harold said:

this is my last comment on PT.

NNNOOOOOOOoooooo!

Lead a protest movement! Start a petition! I’ll sign! But don’t give up without a fight!

I don’t know much about Timothy Sandefur, but it certainly seems strange, on a forum to see a no-comments post that amounts to a plug for a book he contributed to.

Harold, I really hope you don’t go.

I have always thought your presence here has offered keen insights to the minds of the trolls that feed here, and others of their ilk.

As I said before, I hope you don’t go, but if you do, you will be sorely missed.

Harold,

Sorry to see you go. I for one have enjoyed your contributions. Thanks for all the fun discussions. Good luck in all your future endeavors. Do drop by again if you feel the urge.

Great paper. I had always wondered about the inactivation and how it might have come about. Many thanks.

Drop Sandefur!

Bring back Harold!

Panda’s Thumb commenters should make a petition to have Timothy Sandefur removed as a contributer, ASAP. His refusal to allow comments on his entries is wrong. His using his support for evolution as a means of promoting his political views is even more wrong.

And this is flat-out insulting!

http://www.blogger.com/blogin.g?blo[…]logspot.com/

This blog is open to invited readers only http://sandefur.blogspot.com/

It doesn’t look like you have been invited to read this blog. If you think this is a mistake, you might want to contact the blog author and request an invitation.

GET SANDEFUR OFF PANDA’S THUMB!!!

Hear, hear!

We’re mad as hell, and we won’t stand for this anymore!

How do people post entries into PT? Maybe someone can put a couple things up, move Sandefur down…

Henry J said:

But in birds it’s the other way around than it is in mammals?

Yes, and no. It is really quite fascinating. In birds, males are ZZ, while females are ZW. The Z is not homologous to the X. However, there is mixed evidence for dosage compensation in birds. It seems that there may be a few dosage compensated genes, but overall, birds just don’t do much dosage compensation. The rampant gene loss on the W, though, does occur in many bird species, with some exceptions (like the ostrich, and the emu that I talked about earlier here).

fnxtr said:

“the pattern of genes subject to silencing in females among the three classes above is consistent with a process whereby silencing evolves in response to gene loss on the Y chromosome.

Okay, you lost me. If gene g were on both X and Y, and some silencing of g were advantageous, how would you tell if loss in females were a response to a loss on the Y chromosome, and not some other kind of selection?

The loss in females may well have been selected for, to ensure equal gene dosage in both males and females. Please read through the paper. The last part is where we provide evidence that it is gene loss on the Y that is driving silencing on the X (instead of the alternative situation that silencing on the X will result, or allow, gene loss on the Y). In short, we can make hypotheses about how each of these situations are expected to affect the three sets: those with Y-linked “genes”, “pseudogenes”, or “missing”. Because we distinguish between the two latter sets (whereas previous studies just asked whether the Y-linked gene was functional or not), we have additional resolution to ask about the directionality of the process of Y degradation and silencing on the X chromosome.

Just Bob said:

harold said:

this is my last comment on PT.

NNNOOOOOOOoooooo!

Lead a protest movement! Start a petition! I’ll sign! But don’t give up without a fight!

I don’t know much about Timothy Sandefur, but it certainly seems strange, on a forum to see a no-comments post that amounts to a plug for a book he contributed to.

I’ve reconsidered, thanks to some appreciated feedback, including the kindly comments on this thread, but I still consider the offending post I’ve complained about to be absurd.

A comments-blocked plug for a right wing political propaganda book, by someone who endorses an ideology that opposes the basic idea of public education, on a blog devoted to protecting sound teaching of science in public schools. I’ll be generous and call it “undignified”.

In some ideal future when I have time, I may put together a (completely non-political, pathology-related) submission on the role of mutation and natural selection in human cancer (and other cancer, of course). Because as you note, one way to get something off the top is to get something else up there.

harold said:

Just Bob said:

harold said:

this is my last comment on PT.

NNNOOOOOOOoooooo!

Lead a protest movement! Start a petition! I’ll sign! But don’t give up without a fight!

I don’t know much about Timothy Sandefur, but it certainly seems strange, on a forum to see a no-comments post that amounts to a plug for a book he contributed to.

I’ve reconsidered, thanks to some appreciated feedback, including the kindly comments on this thread, but I still consider the offending post I’ve complained about to be absurd.

A comments-blocked plug for a right wing political propaganda book, by someone who endorses an ideology that opposes the basic idea of public education, on a blog devoted to protecting sound teaching of science in public schools. I’ll be generous and call it “undignified”.

In some ideal future when I have time, I may put together a (completely non-political, pathology-related) submission on the role of mutation and natural selection in human cancer (and other cancer, of course). Because as you note, one way to get something off the top is to get something else up there.

Thanks you for reconsidering. Probably best to effect change from within anyway.

harold said:

I’ve reconsidered,

Maybe there is a god after all.

Just Bob said:

harold said:

I’ve reconsidered,

Maybe there is a god after all.

Sorry to keep interrupting the excellent discussion of sex chromosome genetics, but I just made the mistake of going clicking on the one link that Sandefur allows the mere science-supporting peons to view.

The book he is promoting appears to be, as far as I can tell, an overall anti-evolution right wing political propaganda book.

http://www.philosophyblog.com/2013/[…]olution.html

Check this link out. Sandefur and his friend are token “right wing nuts who accept evolution”, included in a book which overall plugs anti-evolution right wing nuttiness. (I’m going to guess that their contribution won’t be an overwhelming scientific defense of evolution, but rather, a mealy-mouthed, plaintive plea that mere acceptance of one aspect of scientific reality not be grounds for ostracism from their “movement” of choice. That’s a guess, and if the book is ever made available to me for free, I’ll be able to see whether or not it is confirmed.)

I think it’s quite unfair that PT provides free, comments-blocked advertising for this anti-evolution book, while refusing to provide the same to Ray Comfort, Ken Ham, Michael Behe, Jonathon Wells, William Dembski, etc.

You mean this bit?

…genetic signals, resulting from the loss of functional X-degenerate genes on the Y, are still accumulating on the X in males to signal the inactivation of one of their X-linked gametologs in females.

Okay, I think I get it now. I wasn’t making the connection to X in males. I forgot I was part girl for a second there.

o_O

Thanks!

Dr. Sayres,

Does your work agree with that of Bryan Sykes at Oxford who asserted that the Y-chromosome is dying quickly. He feels this could lead to extinction in about 100,000 years.

Some have argued that even thought humans reproduce sexually, that Muller’s ratchet applies to Y-chromosomes, and hence it’s unlikely that recovery will happen damaged genes as might be the case where genetic material can be exchanged and mixed from both parents.

Thank you in advance, and congratulations on your publication.

Hi Salvador,

I don’t think that there is clear evidence that the Y will become extinct in 100,000. There are many ways to avoid this. One of which has already occurred on the human sex chromosomes - the addition of a large autosomal segment to both the X and the Y (we call it the X-added or Y-added region). This region is autosomal in marsupials, but sex-linked in eutherian mammals. We have an extra table in the supplement of the paper discussed here that shows that gene loss occurs relatively quickly at first, then seems to slow down. This is consistent with previous work I did looking at substitution rates over evolutionary time in the X/Y-added regions (where we observe that very quickly after recombination is suppressed, the substitution rate increases on the Y, but then it does not continue to increase, at least for the surviving genes).

It is true that Muller’s ratchet applies to the Y chromosomes, but recent work I’m doing now (submitting a revised version in the next few weeks) shows that purifying selection, and specifically background selection, because nearly all of the content on the Y is linked, is quite strong on the human Y chromosome, acting to retain the little content it has left.

But, if we (humans) did “lose” the Y chromosome, we would still survive. The sex-determining region would likely jump to an autosomal chromosome, and the whole wonderful process would start all over again. Or, maybe some other mechanism we haven’t yet anticipated.

Best, Melissa

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This page contains a single entry by M. Wilson Sayres published on May 2, 2013 9:36 AM.

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