Scientists peek at the early evolution of sex chromosomes

Aug 06, 2012
Researchers analyzed the sex chromosomes of papaya, which can produce male, female and/or hermaphrodite flowers. Credit: L. Brian Stauffer and Rishi Aryal

Two new studies offer insight into sex chromosome evolution by focusing on papaya, a multimillion dollar crop plant with a sexual problem (as far as growers are concerned) and a complicated past. The findings are described in two papers in the Proceedings of the National Academy of Sciences.

The research reveals that the sex chromosomes have undergone dramatic changes in their short evolutionary histories (they are about 7 million years old; by comparison, human sex chromosomes began their evolution more than 167 million years ago). One of the two studies compares the papaya X chromosome with that of a closely related non-sex chromosome (called an autosome) in a sister species. The other looks at differences between the X and Y chromosomes.

The studies show that the papaya sex chromosomes are increasing in size – mostly through the accumulation of repetitive sequences – while also reorganizing themselves and losing some genes carried over from their days as autosomes. Some of the lost genes are gone without a trace, while other remnants of genes that are no longer functional – called "pseudogenes" – are still present. The papaya Y chromosome also has independently gained some genes from the autosomes, the researchers report.

Gene loss in the Y chromosome is well documented in ancient Y chromosomes, but gene loss in the X chromosome, particularly at this early stage, is unexpected, as is the expansion of the X chromosome, said University of Illinois plant biology professor Ray Ming, who led both studies.

"The pace of gaining repetitive sequences and losing genes is faster in the Y than in the X chromosome, however," he said.

"This is the first look at an early stage of sex chromosome evolution," said Andrea Gschwend, who conducted the research with Ming while she was a doctoral student in his lab. "Usually people will focus on the ancient sex chromosomes because they are the most relevant to us," she said. "So this is the first direct and complete look at a more recently evolved sex chromosome system."

Analyzing the X chromosome is vital to understanding the evolution of sex, said Ming, an affiliate of the Institute for Genomic Biology at Illinois. The new findings in papaya suggest that the human X chromosome, too, has undergone numerous changes since it first distinguished itself from the autosomes, Ming said. Such changes are not detectable because the ancestral autosomes are no longer available for comparison, he said.

Because the papaya sex chromosomes are young and can be compared to closely related autosomes in a sister species, they offer a view of the early events of both X and Y chromosome evolution, Ming said.

Studying papaya sex chromosomes is a complicated task, however. The papaya has male, female and hermaphrodite sexual types, with two kinds of Y chromosomes (the male Y and the slightly modified, hermaphrodite Yh). Papaya plants may produce combinations of male and female (from the XY system) or hermaphrodite and female (from the XYh system) plants.

This complexity causes problems for papaya growers, Ming said. Hermaphrodites are the most productive of the papaya sexual types and yield the best fruit, but the offspring of hermaphrodites are not all hermaphrodites. To aid growers, Ming and his colleagues aim to develop a "true-breeding" hermaphrodite papaya variety that consistently produces hermaphrodite offspring.

When the researchers compared the X chromosome and the hermaphrodite Yh chromosome, they discovered that two major sequence inversions in the sex-determining regions of the Yh had taken place. One of these inversions occurred about 7 million years ago, and led the and the autosomes down very different evolutionary paths, Ming said. The second inversion occurred about 1.9 million years ago and led to further differentiation between them. Each inversion has also undergone numerous sequence rearrangements, he said.

All of the findings are significant and useful, Ming said, but the , which is generally overlooked in models of sex chromosome evolution, offered the most surprises.

"These studies are changing our view of sex chromosome evolution, particularly X ," he said. "We now know that both the X and Y chromosomes are dynamic in the early stages of their evolution, not only the , as previously thought."

Explore further: Research in rodents suggests potential for 'in body' muscle regeneration

More information: "Rapid Divergence and Expansion of the X Chromosome in Papaya," PNAS, 2012.

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rod_russell_9
1.1 / 5 (16) Aug 06, 2012
It always amazes me when I read unconditional, completely confident statements like your two here ("papaya sex chromosomes ... are about 7 million years old" and "human sex chromosomes began their evolution more than 167 million years ago"). How do you know the age of any sex chromosomes? Thus far, no means of dating events millions of years ago have been proven; they are based only upon assumptions and theories. And there hardly is even a consensus on any of the "mya" calculations. So. when you start out an article in absolutes about ages, instead of stating your source for the time range and an admission that you don't know for sure if any of these ranges are accurate, then you really are wasting your time.
Deathclock
3.5 / 5 (13) Aug 06, 2012
Yet another religious retard here to spread their ignorance of science...

"no means of dating events millions of years ago have been proven; they are based only upon assumptions and theories."

When multiple different dating techniques (including relative dating techniques) all show the same result that is evidence enough that they work correctly, and we have a SHITLOAD of that evidence.

What assumptions? I suppose you mean assumptions that physical rates that have NEVER been observed to vary in all the years we have been measuring them have also remained constant in the past? You're one of those nut jobs that has to assert that physical law, which governs physical rates of change, was significantly different in the past even though there is zero evidence for that and a good deal of evidence to the contrary?

The "only a theory" part is my favorite... whenever I hear that I summarily dismiss anything the person is saying since they are almost certainly just another religiotroll.
Deathclock
3.3 / 5 (12) Aug 06, 2012
FYI "rod_russel", if you knew anything about the various dating techniques used by scientists you would know that they are diverse and each relies on DIFFERENT assumptions. This is significant because they are also MUTUALLY REINFORCED and have been confirmed by dating samples with a known age correctly... we have done this hundreds of times, if not thousands. You would also know that most dating methods have a known margin of error associated with them that is always taken into account by scientists, but not necessarily published in articles intended for the average Rod Russel.
Deathclock
3.3 / 5 (12) Aug 06, 2012
Not only do we know that our methods of dating are accurate to within a margin of error, we know what that margin of error is and the preponderance of these diverse methods serves as evidence that rates of physical change, and therefore physical law itself, has not deviated over time, and we have never observed them to deviate over time.

So, essentially, you couldn't be more wrong.
rod_russell_9
1 / 5 (15) Aug 06, 2012
So, Deathclock, are you a serious scientist or just a roaming bigot?
Phil DePayne
1 / 5 (3) Aug 06, 2012
Haha rod russell is obviously a feminist deathclock, not a religious numbskull
kochevnik
3.5 / 5 (11) Aug 06, 2012
@god_hustle_swine So, Deathclock, are you a serious scientist or just a roaming bigot?
If being factual is bigotry, I'll choose "bigotry". And now you need to acquire a skill. Being willfully retarded is no way to go through a recession.
kevinrtrs
1.3 / 5 (14) Aug 07, 2012
@deathclock - are you seriously unaware of how dating methods are actually applied in real life?
In many if not all cases, it's the ruling paradigm that overrules the actual dates chosen to represent the age of some object. You can see this kind of nonsense with one piece of fossil being announced sensationally older than another - only to have that age disputed and retracted because of "re-work" or some or other contamination when it would obviously upset the evolutionary applecart.
Furthermore, just how do YOU know that the physical rates have been a constant over the millions of years? Were you there to observe them all this time? Was there ANYONE there to observe that they stayed the same?
Just recently a number of confirmed experiments showed that the rates can vary all by themselves - even if by a very small percentage. Which means that the basic assumption of constant decay rate is now down the tubes.
Also - these methods cannot tell the age of new rocks from volcanoes!!!
kochevnik
3.4 / 5 (10) Aug 07, 2012
kevinrtrs stop punishing the rest of the world for your crap public-school red-state 'education.'
rod_russell_9
1 / 5 (10) Aug 07, 2012
kevinrtrs, don't both them with any actual research evidence, they are evolutionary scientists.
Deathclock
3 / 5 (10) Aug 07, 2012
Furthermore, just how do YOU know that the physical rates have been a constant over the millions of years?


I told you... preponderance of the evidence. Different dating methods that rely on different rates of change all agree with each other... all the time. Do you not understand how mutual reinforcement of independent lines of evidence works?

Couple that with the fact that we have been studying these things for some time now and we have never observed them to change... so why should we assume that they do? We should ASSUME what we OBSERVE, and look for evidence otherwise, unfortunately (for you) the evidence also points to constant rates of change and constant physical laws.
Deathclock
3.2 / 5 (11) Aug 07, 2012
Were you there to observe them all this time? Was there ANYONE there to observe that they stayed the same?


This is something a stupid creationist says, are you a stupid creationist? You have to be stupid to say this, because it is OBVIOUS that you don't need to witness something to collect factual information about it... this is the basis of the ENTIRE study of Paleontology, and most of Geology, and most of History... and this also plays a large roll in all of the other physical sciences as well.

You also have to be a stupid creationist to make this argument because it can so easily be turned and used against you... were YOU there to SEE Jesus walking on water, or giving sight to the blind, or rising from the dead? NO, you were not, so how do you YOU know it happened? There is FAR greater evidence for what I (and all scientists) believe than for what you believe. Sorry, but you're a fool for making arguments that apply to yourself more than to your opposition.
Deathclock
3.2 / 5 (11) Aug 07, 2012
Just recently a number of confirmed experiments showed that the rates can vary all by themselves - even if by a very small percentage. Which means that the basic assumption of constant decay rate is now down the tubes. Also - these methods cannot tell the age of new rocks from volcanoes!!!


Oh please do link me to the AIG or ICR article that you read wherein a creationist doesn't have any idea how to use the dating technique that they are trying to use and draws erroneous conclusions... or do you want me to link to one, because I've read several. I like the one by the ICR trying to use fission track dating to prove the Earth is young, and not realizing that latent heating of the specimen serves to "reset the clock" on fission tracks and that this is why they are useful as a lower bound only and then coming to an incorrect age (which is still FAR older than 6000 years) and proclaiming victory like a goddamn idiot.

Yeah, I've read those articles.
kochevnik
3.2 / 5 (9) Aug 07, 2012
@fraud_hustle_swine, Don't both them with any actual research evidence, they are evolutionary scientists.
As opposed to what other kind of scientists? You do know you're on a SCIENCE site, yes? Your fellow freepers must be missing you.
Deathclock
3.4 / 5 (10) Aug 07, 2012
And finally kevin, you're only talking about radiometric dating techniques, there are other dating techniques, and these are used in conjunction with each other whenever possible to either mutually affirm one another or to identify mistakes (mistakes do of course happen, no one is perfect).

Your problem is you think of everything in terms of absolutes, science does not. When we date something using 3 or 4 different methods and those methods roughly agree with each other then we have an estimate of the age of the sample to within a known margin of error. No scientist has ever claimed to know, TO THE YEAR, how old something is that is millions of years old... we might know to within a few tens of thousands of years, maybe to within a hundred thousand years, and when talking about a sample of > 100,000,000 years it's not that significant.

http://www.talkor...specific
Deathclock
3 / 5 (8) Aug 07, 2012
Oops, I said finally too soon, I also wanted to quickly make the point that, again, mistakes do happen, but for every mistake that you hear about, or for every instance of one date being overturned later by another date, there are THOUSANDS of samples being dated that you never hear about... you ONLY hear about the mistakes, and you never hear about the dates that are never found to be mistaken, so you think that the techniques are wrought with problems when they are not. INDIVIDUALS make mistakes and apply incorrect dating techniques for the sample in question or don't take relevant factors into account when applying the correct techniques, but this happens rarely.

It's as if you read occasionally that an airplane has crashed so you think that airplanes always crash, but you don't realize that thousands of airplanes arrive at their destination safely every day.

This is a type of bias and the name is escaping me right now... not confirmation bias but something else...
Deathclock
3.4 / 5 (10) Aug 07, 2012
Also, I wanted to point out, that certain forms of radiometric dating (C14) are allowed to be used as evidence in a court of law... I don't know who you think you are to know better than all scientists AND the entire legal community, but you must be one hell of an individual that should clearly be supreme ruler of Earth if your opinion trumps ALL of theirs!
antialias_physorg
4.6 / 5 (11) Aug 07, 2012
Furthermore, just how do YOU know that the physical rates have been a constant over the millions of years? Were you there to observe them all this time?

Actually, yes. When you look through a telescope you look into the past (because light takes time to travel). If physical constants would have been significantly different in the past then we'd be seeing significantly different types of stars/material in the early universe. So we can be fairly sure that physical laws haven't changed radically - at least since the time of recombination (which is as far as we can look back).

If there had really been a radical change we wouldn't be seeing any stars at all from the early universe, because either matter would not have formed at all under such conditions or fusion could not have started.
kochevnik
3.4 / 5 (10) Aug 07, 2012
This is a type of bias and the name is escaping me right now... not confirmation bias but something else...
It's selection bias. More generally, christers prefer research that supports a predetermined outcome.
Deathclock
3 / 5 (8) Aug 07, 2012
That's the one, thank you.
Deathclock
3 / 5 (8) Aug 07, 2012
Actually, it is selection bias, but I was referring to unintentional selection bias due to only failures being publicized in the mass media. Without knowledge of how many successes their are, and only ever hearing about the failures, many people assume that there is a real problem. There are many of examples of this, if you hear about kidnappings on the news with semi-regularity you'll begin to think that kids are being snatched up left and right, but that's only because the news doesn't report on every time a kid goes to the park and IS NOT abducted...

I know a women (family member) who lives her life in fear because of this. All of the negativity in the news has made her afraid to fly, afraid to drive, afraid to be alone in public, etc...

This applies to mistakes made with radiometric dating as well, it's only ever reported when a mistake is made, but for every mistake there are hundreds of successful applications... which you never hear about.
TheGhostofOtto1923
3.8 / 5 (16) Aug 07, 2012
with one piece of fossil being announced sensationally older than another - only to have that age disputed and retracted because of "re-work" or some or other contamination when it would obviously upset the evolutionary applecart.
Now kev you know full well that 'disputed and retracted' is actually 'reviewed, discussed and refined'. As opposed to biblical fantasy which is never reviewed and refined, except in an apologetic and obfuscatory sense.
Furthermore, just how do YOU know that the physical rates have been a constant over the millions of years? Were you there to observe them all this time? Was there ANYONE there to observe that they stayed the same?
And this is always funny. Claiming that lack of direct observation disproves evolution. And who was there to watch your GOD do these things kevin?

At least evolution has left tons of very solid evidence. God left a book full of crude lies and fairy tales. And absolutely nothing else except SCADS of contrary evidence.
TheGhostofOtto1923
3.7 / 5 (15) Aug 07, 2012
Scads of CONTRARY evidence Kevin. All we had to do was go out and dig in the sand, examine the world and our bodies closely, to realize that your book in nonsense. This becomes more obvious every day.

And why WOULD a god create a world which is so obviously contrary to the description he wrote of it? How can you ponder THAT question without concluding that the god of your book CANNOT exist?

I know - you all say it takes faith to understand what god wrote. But as we know, faith is belief despite evidence. With faith you can read gullivers travels, or the phone book even, and conclude that god exists for us to serve right? I am sure god is listed in there somewhere.

I am waiting to hear what you have to say when Curiosity finds fossils on mars. That will be interesting.
Deathclock
2.1 / 5 (7) Aug 07, 2012
Faith is believing something so strongly that no amount of evidence or reason can convince you otherwise. Faith is not caring about the truth, only that you maintain your belief in the face of all opposition. Faith is fundamentally irrational and should be considered a mental illness.
TheGhostofOtto1923
3.7 / 5 (12) Aug 07, 2012
Faith is believing something so strongly that no amount of evidence or reason can convince you otherwise. Faith is not caring about the truth, only that you maintain your belief in the face of all opposition. Faith is fundamentally irrational and should be considered a mental illness.
Uh that's what I said. With more eloquence and far fewer words.
JVK
1 / 5 (2) Aug 07, 2012
Does the evolution of sex chromosomes in any species appear to be linked to random mutations? If not, what does an article like this do to the faith of people in random mutations theory? Similarly, what does the report on 'Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor' (Kochman, 2012) tell the evolutionary theorists in words that clearly state: "The discovery of the fact that one decapeptide molecule, among the GnRHs, was constructed perfectly at the beginning of 400 million years evolution and that it is not possible to improve its physiological potency using the any natural amino acid is, in my opinion, important, fascinating and beautiful."

GnRH controls the species-specific hormone-dependent development of our neuroendocrine and neuroimmune systems, which enable brain development that is dependent on both nutrient chemicals and pheromones, as is the behavior of other organisms from microbes to man. What evidence supports faith in random mutations?
Deathclock
1.8 / 5 (5) Aug 07, 2012
"random mutations theory?"

What?

You realize we can see mutations occur, right? This stuff is proven and put into practice daily.

Regarding the quote about being constructed "perfectly" 400 million years ago... "perfectly" is meaningless. Perfectly for it's current use, perfectly for the current environment? Great, but things change. Also, evolutionary theory already agrees that things can become optimized to the point that no further optimization can occur so long as the environment remains unchanged, this isn't news.
Calenur
2 / 5 (4) Aug 07, 2012
Nicely done guys....I was going to jump on kevin and rod, but you guys went full face-ripper monkey on them.
JVK
1 / 5 (2) Aug 07, 2012
"random mutations theory?"

What?

Regarding the quote about being constructed "perfectly" 400 million years ago... "perfectly" is meaningless. Perfectly for it's current use, perfectly for the current environment? Great, but things change.


What RANDOM mutations (or changes in the environment) caused the advent of sexual reproduction in yeasts, which continued via the conserved molecule of GnRH across 400 million years of vertebrate evolution? The operative word here is RANDOM not mutations, which is why I clearly stated my interest in "random mutations theory."

What evidence supports faith in random mutations?
kochevnik
1 / 5 (4) Aug 07, 2012
@JVK What evidence supports faith in random mutations?
Sorry you failed fractals and chaos theory. There are specific genes that, when activated, amplify chaos to augment oncogene diversity. For an example, study CANCER you nitwit.

I have little expertise in biology, yet I grasp that principle from maths.
JVK
1 / 5 (2) Aug 07, 2012
There are specific genes that, when activated, amplify chaos to augment oncogene diversity. For an example, study CANCER you nitwit.

I have little expertise in biology, yet I grasp that principle from maths.


Only a nitwit would propose that cancer is involved in adaptive evolution. Besides, there is evidence that at least some cancers are genetically predisposed and epigenetically effected by nutrient chemicals and environmental toxins like endocrine disruptors. Exposure to nutrient chemicals is not random; exposure to endocrine disruptors that might cause cancer may be random or a matter of choice when exposure is linked to reward mechanisms. But the reward mechanisms also are genetically predisposed. What part of random mutations theory are you saying is not random? Which specific genes that, when activated, amplify chaos to augment oncogene diversity are included in random mutations theory?
Torbjorn_Larsson_OM
3.4 / 5 (5) Aug 08, 2012
Creationists shouldn't comment on science, it is hilarious to see.

Recap of the gish gallop:
- Dating; and dating again. We have many independent and even self calibrating methods.
- "Assumptions". Science don't do assumptions, it uses testable constraints which obviously is a totally different kind of beast. Say the age of the Earth - no gene should be older if it evolved here.
- Bigotry. Creationism is anti-science since it rejects facts and wishes them to be replaced with faith. There is no bigotry in defending science against religionistas.
Torbjorn_Larsson_OM
3 / 5 (4) Aug 08, 2012
- "Random mutations". Evolution isn't "random" or "mutations", but the process taking living populations to living populations through heredity. Here from papaya with smaller sex chromosomes in the past to today's sizes, both sizes of which are observed in the genome.

Mutations, one among several sets of mechanisms in evolution, isn't "random" in anything but the sense that it is often stochastic mechanisms. It is for example not equi-probable, which is the common sense of ill-defined "random".

Mutation is one source of variation, and variation is theoretically and observably uncorrelated with selection. "Natural selection imposes direction on evolution, using undirected variation." I.e. selection can be deterministic, but its result is always contingent on variation and other factors.

The deterministic property of evolution can be witnessed every time a new function evolves out of variation.
Deathclock
1.8 / 5 (5) Aug 08, 2012
Right, even if you agree that variation is random (which I think it is to some degree, if not equi-probable as you said) it's still important for everyone to understand that selection is absolutely not random.

The analogy I like to use is if you were handed a random lego block every five seconds and you could choose to use that lego block to improve your model or to discard it... The random lego block you receive is from variation (which includes inheritance and mutation) and the decision you make whether to use that block or not is selection. That's how evolution takes a random source of variation and results in a non-random and directed outcome.
JVK
1 / 5 (4) Aug 08, 2012
Natural selection is for nutrient chemicals and pheromones. Both alter intracellular signaling and stochastic gene expression. Nutrient chemicals are essential to an organism's survival. Pheromones control reproduction. In vertebrates the effect of pheromones on hormones and behavior can be traced to the same molecule: GnRH, across 400 million years of adaptive evolution via ecological, social, neurogenic, and socio-cognitive niche construction. These facts defy anyone who thinks they can support their theory about adaptive evolution or undirected variation that might possibly be due to anything but food acquisition and pheromones. So go ahead you silly theorists, make my day. How did sex chromosomes evolve in papaya or any other species, and why?
Vreejack
3.7 / 5 (3) Aug 11, 2012
There aren't any "silly theorists" here, just curious people. If you really want to know how sex chromosomes evolve why don't you look it up yourself? I found dozens of articles in 0.6 seconds.