Genes for limbs existed prior to there being actual limbs

[Fire Fly]

Link

New Genetic Data Overturn Long-Held Theory Of Limb Development (5/27/2007)
-United States

Long before animals with limbs (tetrapods) came onto the scene about 365 million years ago, fish already possessed the genes associated with helping to grow hands and feet (autopods) report University of Chicago researchers in the May 24, 2007, issue of Nature.

This finding overturns a long-held, but much-debated, theory that limb acquisition was a novel evolutionary event, requiring the descendents of lobed-fin fish to dramatically alter their genes to adapt their bodies to their new environments of streams and swamps.

The paper, "An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish," shows that the genetic and developmental toolkit that builds limbs with fingers and toes was around long before the acquisition of limbs, according to the scientists, and that this toolkit exists in some primitive form in a living primitive bony fish, the paddlefish.

"We found that the genetic capability seen in tetrapods to build limbs is present in even more primitive fish," said lead author Marcus Davis, PhD, a postdoctoral fellow in Neil Shubin's lab at the University of Chicago.

Instead of using zebrafish--the hallmark animal for laboratory development studies--the scientists used paddlefish as a proxy for a more primitive ancestor. Unlike the simple fins of zebrafish, paddlefish have an elaborate fin skeletal pattern similar to that seen in more primitive vertebrates such as sharks and many fossil fish. This sturgeon-type fish is farm raised for caviar, which gives scientists relatively easy access to the animal for study.

The fin of paddlefish resembles that of zebrafish. The interior arrangement is the same, but the back part of the paddlefish fin has longer elements. Accepted theory among scientists has been that the pattern of Hox gene expression seen in zebrafish represents the primitive condition for the fin in any vertebrate, and the group leading to tetrapods elaborated on this Hox expression by adding a second phase and added to the skeletal pattern.

The scientists studied the development of paddlefish fins to test whether the genes activated to make hands and feet in tetrapods were different from the genes activated to make fish fins. Davis working with postdoctoral fellow Randall Dahn, PhD, and Shubin, PhD, professor and associate dean for organismal and evolutionary biology at Chicago and provost of the Field Museum, disproved conventional wisdom.

The team looked at Hox genes--which play a vital role in limb development--in the pectoral fins of paddlefish. To track where the Hox genes are active in the fin, the team inserted molecular markers and showed the activity pattern has similarities to patterns of these same genes in tetrapod limbs.

Tetrapods have a second phase of Hox gene expression that happens later in development. During this second phase, hands and feet develop. Although this second phase is not known in zebrafish, the scientists found that it is present in paddlefish, which reveals that a pattern of gene activity long thought to be unique to vertebrates with hands and feet is in fact much more primitive.

This is the first molecular support for the theory that the genes to help make fingers and toes have been around for a long time--well before the 375-million-year-old Tiktaalik roseae, the newly found species discovered in 2004 by Shubin and colleagues. Tiktaalik provided a missing evolutionary link between fish and tetrapods and was among the first creatures that walked out of water onto land.

Prior to this find, scientists had little evidence of where the wrist came from. A popular theory, one Shubin himself subscribed to, was that it was a novel development--that genetic variance gave rise to an entirely new function.

What Tiktaalik revealed morphologically, Shubin, Davis and Dahn have proven genetically.

"This report provides important new information about the evolution of hands and feet in vertebrate animals," said Lance Grande, PhD, head of collections and research at the Field Museum.

Scientists have attacked the evolutionary quandary of limb development on two fronts: the direct evidence of the fossil record and the morphology, and its relationship with specific genetic mechanisms. What they needed, Davis said, was an animal "unmolested by time."

"When you try to directly compare zebrafish fins and tetrapod limbs, it's like comparing apples to oranges because each retains portions of the skeleton lost by the other," he said. "Just as tetrapods went off and did something crazy with their fin by adding to it, zebrafish went off and did something crazy by losing part of their fin.

"So the innovation here is about a pattern of loss of gene activity [for the zebrafish] and not a pattern of acquisition [for tetrapods]," he said.

Although this pattern of genes clearly helps to make hands and feet today in tetrapods, that may not be their original intent, Shubin said. "Here's a fish that doesn't have an autopod but is still using those genes in a second phase to help pattern out a fin that doesn't have fingers, never did, and is very far removed from tetrapods."

The capability of building limbs with fingers and toes existed for a long period of time, but it took a set of environmental triggers to make use of that capability.

According to Shubin, in the Late Devonian, animals like Tiktaalik and its descendants acquired limbs with fingers using this primitive design, largely because their ecosystem--the small streams that they lived in--was new.

"It had the tools," he said, "but it needed the opportunity as well."

The Shubin lab has expanded its studies to see if the Hox gene expression is present in yet older common ancestors. The research team now is studying the primitive fin development of sharks.

Bolded by me.

[General Zod]

Sadly I see the fundies latching onto this one as proof that we were designed.

[Enforcer Talen]

Hm. Does that mean that, with the right trigger, we might activate other genes?

[K. A. Pital]

It's interesting if we have some hidden genetic abilities.

Heh. How long till this hits AiG?

[wolveraptor]

I don't see why fish would've developed the genes necessary to grow more powerful limbs if there was no environmental pressure to grow them. It's not like evolution could prepare them for what was ahead. It's reactive, not proactive, so to speak.

[Turin]

I don't see why fish would've developed the genes necessary to grow more powerful limbs if there was no environmental pressure to grow them. It's not like evolution could prepare them for what was ahead. It's reactive, not proactive, so to speak.

There's a certain amount of random genetic drift in "inactive" genes. When these genes are one with such dramatic on-off effects (like Hox, which in fruit flies can causes feet to grow where their antennae should be with a single nucleotide polymorphism), it's not all that crazy to think of. We're talking limbs with extra joints here, not suddenly growing more muscular limbs.

[Turin]

Ghetto edit:

There's a certain amount of random genetic drift even in "inactive" genes.

[ArmorPierce]

Sadly I see the fundies latching onto this one as proof that we were designed.

I could see that happening but that just because they're stupid. In reality this makes evolution just that much more realistic because you don't just one day randomly pop out with the genetic information for a hand growing off the side of your chest randomly and the lack of "transitional phase" like half such as useless studs slowly growing out of your side eventually becoming a hand.

[Coyote]

Ignorant science question-- is there such a thing as cell & DNA fossils that can be studied to see if things like, for example, trilobites had something like this?

[Academia Nut]

Unfortunately that's unlikely as fossilization tends to destroy DNA, which was why that story about finding soft tissue in a T Rex bone last year was such big news.

As to the article here, I would hazard to guess that the genes may have come from an earlier organism that may have crawled along the bottom of the ocean before switching over to swimming, before switching back over to crawling, only this time on land instead.

[wolveraptor]

As to the article here, I would hazard to guess that the genes may have come from an earlier organism that may have crawled along the bottom of the ocean before switching over to swimming, before switching back over to crawling, only this time on land instead.

That seems more plausible than this being the result of random genetic drift, to my uneducated mind at least.

We're talking limbs with extra joints here, not suddenly growing more muscular limbs.

Joints are complicated structures, more so than the simplistic legs of most insects, which are little more than struts or stilts. They couldn't possibly be developed by a single mutation. It would need to be an accumulation of them.

[Erik von Nein]

As to the article here, I would hazard to guess that the genes may have come from an earlier organism that may have crawled along the bottom of the ocean before switching over to swimming, before switching back over to crawling, only this time on land instead.

That's certainly plausable, since there are quite a few species that do that today. Of course, you'd need to show how they went from swimming to crawling to swimming agian.

[Grandmaster Jogurt]

Joints are complicated structures, more so than the simplistic legs of most insects, which are little more than struts or stilts. They couldn't possibly be developed by a single mutation. It would need to be an accumulation of them.

"Little more than struts or stilts"? Insect legs are fairly elaborate; hell, insects are part of the phylum Arthropoda, which is named for its jointed legs.

[Academia Nut]

As to the article here, I would hazard to guess that the genes may have come from an earlier organism that may have crawled along the bottom of the ocean before switching over to swimming, before switching back over to crawling, only this time on land instead.

That's certainly plausable, since there are quite a few species that do that today. Of course, you'd need to show how they went from swimming to crawling to swimming agian.

Swimming to crawling to swimming? While that is possible, I meant that their lineage started more or less as crawlers. Apparently early fish evolution isn't very well known and it wasn't until the development of bony jaws that they truly started to develop, thus without a more complete fossil record much of the history is mere conjecture and hypothesis. Depending on what this new data shows, scientists might have to shuffle the hagfish and lamprey around again, either bringing them closer to true fish or even further out, depending on where the split might have happened.

[wolveraptor]

Joints are complicated structures, more so than the simplistic legs of most insects, which are little more than struts or stilts. They couldn't possibly be developed by a single mutation. It would need to be an accumulation of them.

"Little more than struts or stilts"? Insect legs are fairly elaborate; hell, insects are part of the phylum Arthropoda, which is named for its jointed legs.

I admit I didn't have arachnids, crustaceans and larger insects in mind when I wrote that. Still, they lack the presence of muscles on the extremeties. It's all controlled by muscles at near the body itself. Even larger spiders like tarantulas only use hydraulics to move their legs. It's nowhere near as complex as a flexible mammal's limb.

[R. U. Serious]

I don't see why fish would've developed the genes necessary to grow more powerful limbs if there was no environmental pressure to grow them. It's not like evolution could prepare them for what was ahead. It's reactive, not proactive, so to speak

Agreed, I think this potential misrepresentation could be due to the fact that it's a press-release by the University, which are often written by people that are not involved in the reasearch or the research areas themselves.

I think what's really going on (and how the article hould be read) is that it was discovered that the same genes that are responsible for the development of fins adapted and became responsible for the development of limbs. Whereas up until before the study it was assumed that the genes reposnsible for limbs were entirely new genes.

THe press release talks about the "genetic capability" to grow limbs, which I assume is entirely different from what we would commonly understand if we just said "capability to grow limbs". That is probably meant to signify that it was the same genes, not imply any "foresight" in evolution, nor that limbs had been developed at some earlier point and then disappeared again.

[Turin]

As to the article here, I would hazard to guess that the genes may have come from an earlier organism that may have crawled along the bottom of the ocean before switching over to swimming, before switching back over to crawling, only this time on land instead.

That seems more plausible than this being the result of random genetic drift, to my uneducated mind at least.

We're talking limbs with extra joints here, not suddenly growing more muscular limbs.

Joints are complicated structures, more so than the simplistic legs of most insects, which are little more than struts or stilts. They couldn't possibly be developed by a single mutation. It would need to be an accumulation of them.

Let me step back a minute here. Assuming the article is actually accurate (which admittedly is always an issue with science press), this doesn't contradict anything we already know.

We know that things like the number of joints or number of digits in a limb can be controlled by very small genetic changes. This shouldn't be all that surprising. Look at segmentation in worms (this is an example Richard Dawkins uses a lot). Once you have the genetic recipe for one segment, all you need then is code that says "make more of those." And once you're making more than one of something, it's even easier because you just have to change the genetic "bit value." As another example, polydacty is estimated to affect 2 out of every 1000 children (with variance by ethnic group, etc.). In this case, we're talking about a bit value change from 5 to 6 in the instructions to the developing fetus for the number of fingers or toes to make per foot.

Upon reflection, I think your initial remarks reflect a bit of leftover Lamarckianism:

I don't see why fish would've developed the genes necessary to grow more powerful limbs if there was no environmental pressure to grow them. It's not like evolution could prepare them for what was ahead. It's reactive, not proactive, so to speak.

Variance exists on its own, without any environmental "pressure." In fact, this natural variance is required for evolution to work. (Yes, this variance always consists of small changes within "genetic space", but as I've illustrated above, we're not necessarily talking about a change of more than a few genetic bits here.) Once the variance occurs, selection pressure decides whether or not the variant is retained and passed on.

In this case, one can easily imagine that a fish born with extra joints in its limbs will be more easily able to get food further up the shore, find safer places to lay its eggs, etc. As long as this added advantage outweighs the energy cost involved in making the extra joints, the advantage will be retained.

[wolveraptor]

Variance exists on its own, without any environmental "pressure." In fact, this natural variance is required for evolution to work. (Yes, this variance always consists of small changes within "genetic space", but as I've illustrated above, we're not necessarily talking about a change of more than a few genetic bits here.) Once the variance occurs, selection pressure decides whether or not the variant is retained and passed on.

I know, but I don't see why this particular variance would've been retained if it were superflous and unnecessary at the time that it was developed, which is what the article seems to imply.

In this case, one can easily imagine that a fish born with extra joints in its limbs will be more easily able to get food further up the shore, find safer places to lay its eggs, etc. As long as this added advantage outweighs the energy cost involved in making the extra joints, the advantage will be retained.

The whole point of this article is that fish had the capability to grow these joints long before there was fertile land for them to climb up on to in the first place. It's easy to concieve of a fish that develops limbs in the scenario you outlined. It's harder when there is no possible use for those limbs at the time they're gained.

[Turin]

I know, but I don't see why this particular variance would've been retained if it were superflous and unnecessary at the time that it was developed, which is what the article seems to imply.

I can see your argument over why the article implies this, but it's explicitly mentioned that it's not superfluous:

Although this pattern of genes clearly helps to make hands and feet today in tetrapods, that may not be their original intent, Shubin said. "Here's a fish that doesn't have an autopod but is still using those genes in a second [developmental] phase to help pattern out a fin that doesn't have fingers, never did, and is very far removed from tetrapods."

Emphasis and "[developmental]" clarification mine. The modification has a use in non-tetrapods, otherwise we wouldn't still see it in the paddlefish. The improvement may be subtle, but that's exactly what we expect in evolutionary changes. I guess my previous example wasn't very good because it dealt with walking, but let's change it to an example wherein the fish with extra joints in its fins can turn more quickly or swim faster than its ancestors. Clear advantage, one that can be passed on to descendants, and one that has nothing to do with walking.

This (nearly undecipherably technical) article on development of fins in paddlefish illustrates what we're talking about. The fin develops in a fashion that is vaguely similar to a hand inasmuch that the skeletal structure separates out in a similar fashion. What's interesting, and why the article is newsworthy, is that the genetic changes that made this fin improvement possible happened longer before the development of land-going fish than was previously thought. If anything, this means that the journey from "genetic shift in skeletal configuration" to "crawling out on land" happened more gradually than originally suspected.

[wolveraptor]

Ah, I see. Point conceded. I guess I misinterpreted the article.

[Turin]

Ah, I see. Point conceded. I guess I misinterpreted the article.

I don't think it's just you, though... the article is pretty poorly written, if you ask me. Unless you read it very closely you could be easily lead down that path. Still cool research, though.

[Cykeisme]

My understanding is poor, but I have a question as to whether the following is a possibility:

Could the genetic data (in the "junk" genes) for multiple joints ("limbs") have actually arisen on rare occassion among the purely water-dwelling fish?

I imagine it would have conferred neither advantage nor disadvantage in this case (at least not significantly), so these mutants could have popped up here and there, but not mattered much, especially it wasn't a dominant trait.

When environment changed to favor the multi-joined limbs, the limby mutants became king, jogged all over their finned brothers and sister, had way more kids, and basically took over.

Possible?

[Turin]

Could the genetic data (in the "junk" genes) for multiple joints ("limbs") have actually arisen on rare occassion among the purely water-dwelling fish?

I imagine it would have conferred neither advantage nor disadvantage in this case (at least not significantly), so these mutants could have popped up here and there, but not mattered much, especially it wasn't a dominant trait.

When environment changed to favor the multi-joined limbs, the limby mutants became king, jogged all over their finned brothers and sister, had way more kids, and basically took over.

Possible?

1. The genetic data for what would become limbs wasn't in "junk" genes, because it finds itself expressed in the development of additional joints in the fins.
2. This sort of genetically small variant is what one expects to happen, in order to create the variance in individuals that is the driver of natural selection.
3. For the trait to be retained, the selection environment has to favor the variation, so this isn't a case where it confers neither advantage or disadvantage.

So in this particular case, what you're talking about doesn't appear to be true.

That being said, there is a certain amount of random "drift" in intron DNA (genetic information that doesn't code for anything) due to sexual recombination and point mutation. Any arbitrary stretch of DNA can be switched with its allele in sexual recombination (at a rate inversely proportional with its length, obviously). If this happens at the introns, which is increasingly likely the bigger your genome gets, you have drift in DNA without it being expressed in the individual.

The problem with the scenario you've illustrated is that there's very little chance that this new variant will be retained for any real length of time, because it's potentially subject to random drift again with the very next generation, and there's no selection pressure either way because it's non-coding. The shorter the length of the random piece, the longer it's likely to be retained by random chance, but the less chance it has of being even remotely useful at any time in the future because it contains little genetic data.

Make sense?

[Cykeisme]

So there had to be reason for multi-jointed fins to be more successful (by conferring some sort of advantage in the current environment) right from its first appearance?

[Turin]

So there had to be reason for multi-jointed fins to be more successful (by conferring some sort of advantage in the current environment) right from its first appearance?

I suppose in theory if the multi-jointed fins had no additional cost in energy to build, you could have them float around for a while without having an advantage and the multi-joint vs single-joint alleles would randomly drift. But in reality, every variation in nature is going to have either a selection advantage or a sexual selection advantage.

Now, that being said, the advantage is usually very slight, which is why it takes a long time for a variation to take hold across a larger population.