Genetic evidence for punctuated equilibrium

The Scientist ^ | 06 October 2006 | Melissa Lee Phillips

[PatrickHenry]

Evidence for punctuated equilibrium lies in the genetic sequences of many organisms, according to a study in this week's Science. Researchers report that about a third of reconstructed phylogenetic trees of animals, plants, and fungi reveal periods of rapid molecular evolution.

"We've never really known to what extent punctuated equilibrium is a general phenomenon in speciation," said Douglas Erwin of the National Museum of Natural History in Washington, D.C., who was not involved in the study. Since its introduction by Stephen Jay Gould and Niles Eldredge in the 1970s, the theory of punctuated equilibrium -- that evolution usually proceeds slowly but is punctuated by short bursts of rapid evolution associated with speciation -- has been extremely contentious among paleontologists and evolutionary biologists.

While most studies of punctuated equilibrium have come from analyses of the fossil record, Mark Pagel and his colleagues at the University of Reading, UK, instead examined phylogenetic trees generated from genetic sequences of closely related organisms.

Based on the number of speciation events and the nucleotide differences between species in each tree, the researchers used a statistical test to measure the amount of nucleotide divergence likely due to gradual evolution and the amount likely due to rapid changes around the time of speciation.

They found statistically significant evidence of punctuated evolution in 30% to 35% of the phylogenetic trees they examined. The remaining trees showed only evidence of gradual evolution.

Among the trees showing some evidence of punctuated equilibrium, the authors performed further tests to determine the size of the effect. They found that punctuated evolution could account for about 22% of nucleotide changes in the trees, leaving gradual evolution responsible for the other 78% of divergence between species.

Pagel and his colleagues were surprised that rapid evolution appears to contribute so much in some lineages, he said. "I would have maybe expected it to be half that much," he told The Scientist.

The researchers also found that rapid bursts of evolution appear to have occurred in many more plants and fungi than animals. Genetic alterations such as hybridization or changes in ploidy could allow rapid speciation, Pagel said, and these mechanisms are much more common in plants and fungi than in animals.

"Their result is pretty interesting, particularly the fact that they got so much more from plants and fungi than they did from animals, which I don't think most people would expect," Erwin told The Scientist.

However, it's possible that the analysis could be flawed, because the authors didn't take into account extinction rates in different phylogenetic trees when they determined the total number of speciation events, according to Douglas Futuyma of the State University of New York at Stony Brook, who was not involved in the study. But "they've got a very interesting case," he added. "I certainly think that this warrants more attention."

According to Pagel, the results suggest that other studies may have misdated some evolutionary events. Dates derived from molecular clocks assumed to have a slow, even tempo will place species divergences too far in the past, he said, since genetic change assumed to take place gradually may have happened very quickly.

"These kinds of events could really undo any notion of a molecular clock -- or at least one would have to be very careful about it," Futuyma told The Scientist.

Well known evolutionary mechanisms could account for rapid genetic change at speciation, Pagel said. Speciation often takes place when a population of organisms is isolated, which means that genetic drift in a small population or fast adaptation to a new niche could induce rapid evolutionary change.

=======
[Lots of links are in the original article, but not reproduced above.]

[azhenfud]

The researchers also found that rapid bursts of evolution appear to have occurred in many more plants and fungi than animals. Genetic alterations such as hybridization or changes in ploidy could allow rapid speciation, Pagel said, and these mechanisms are much more common in plants and fungi than in animals.

"Their result is pretty interesting, particularly the fact that they got so much more from plants and fungi than they did from animals, which I don't think most people would expect," Erwin told The Scientist.

---

Reckon pollination is mostly to blame?

[azhenfud]

While digging irrigation ponds at the family farm, we used to dig up or uncover petrified wood along with arrowheads.

[grey_whiskers]

I've been watching mythbusters and on that "revolution in Iran" thread...

Do you have a link for your guy who modeled fitness landscapes?

That'd be like the "ultimate" in cool...

...Besides, it'd be fun to do sensitivity analysis on it, or to debug his code ;-)

Cheers!

[SoldierDad]

Then when you have separated, via line and time, it becomes pretty obvious what changes have occurred, and yes, they have become completely different species.

Or, they were always different species of animals unrelated except for where they lived.

[SoldierDad]

Oh, so the courses I took in college which presented the "evidence" for the TOE wasn't good enough! I need to receive and "education" from some toad on the internet.

[SoldierDad]

You may stick your head in a bucket of ice water.

[null and void]

Do you have a link for your guy who modeled fitness landscapes?

Not quite:

Will Wright is featured in one of the articles of the August 2006 edition of Discover Magazine

I believe that a derivative of this is one of the core algorithms in the game "Spore", which is coming out next year.

[Coyoteman]

Oh, so the courses I took in college which presented the "evidence" for the TOE wasn't good enough! I need to receive and "education" from some toad on the internet.

Knowledge is knowledge. The source is not the issue. The accuracy of that information is what is important.

Many facts have been added, and details changed, in the theory of evolution since you (and I) were in school. But the theory itself has only been supported; the additional details and facts have expanded the theory, not contradicted it. The theory is currently stronger than ever.

[SoldierDad]

Ah, the insults begin. Seems to demonstrate the existance of lower life forms.

[SoldierDad]

"If Creationism was true, we would have to believe that modern humans walked with Dinosaurs and swam with the Trilobites, right? I would have to believe that all the animal species that exist today, existed at the creation of the Earth, right? I never made the claim of being a "creationist". At least not of those who proclaim the Earth is only 6000 years old, and that all animal species (including humans) "became" at the same time. My question doesn't have anything to do with whether or not living organisms "evolved". I have no problem with that tenent of TOE. I just don't see where a specific animal species changed such that it became something entirely different (which is what many evos propose).

[EternalVigilance]

I should have learned long ago never to interupt an evo church service.

[RunningWolf]

Hey how is your son doing? That is much more important right now.

In 1971 I was enlisting for combat arms mos in the US Army but backed out at the last minute, so now I am a 'wannabe VietVet'. In 1971 and '72 the conflict had shifted more into Laos and Cambodia, more Laos IIRC. This was not widely reported then, most likely that is where I would have ended up.

This is a totally different war they are fighting over in Iraq than we would have back in the 70's. That is obvious of course. We did not have near the personal protections, or the powers of some of the new weaponry available to us, but we were not faced with the humongous IED in a urban environment either.

But back to the debate.That some men believe and assert as a reality that all men have come from some ephemeral ape ancestor really means nothing to me (nor does it bother me) save for where to from that concept that some among them want to lead.

I don’t get the 'janitor' denigration either, unless it is the inference that academic recognition is some sort of value judgment on a mans life and contribution to the world.

That might be an interesting topic to research.

W.

[SoldierDad]

When one looks at it Creationism falls apart from a scientific standpoint. There just isn't any evidence that all species were created at once, or even within a hundred million years of each other.

If we were to consider just for one moment that God did indeed "create" all life on Earth, why would anyone think that He had to have "created" all life forms at the same time? Would it not be possible that God started off with those earlier life forms, and then over various periods of time (separated by lengthy periods) He "created" different life forms? What you call "explanations" are merely guesses of what happened which fit the "evidence" as humans understand the "evidence" Guesses can never be proof as any scientist worth their degree will attest.

[SoldierDad]

I honestly don't know how my son is doing now. If you notice my new tagline You'll see where he's located. There was a post on FR regarding the 10th Mountain Division tonight, and where their AO now is. We have not heard from him since the email he sent last Tuesday morning. The new AO for the 10th must not be a very safe place, because my son told his brother not to let my wife and I know where he was moving to in a phone call he made about 12 days ago.

I served in the Air Force in the mid to late 70's, and was stationed at Minot AFB in a Security Police Squadron. Same job my dad did during the Korean conflict (though he was never deployed to Korea). My brother was an Army Ranger right at the end of Viet Nam, but also was not deployed to the war. Right now we have my son and my nephew (my brother's son) in Iraq. A close friend's daughter is also in Iraq. Our family has served in the U.S. military since the Revolutionary War, and we've had a family member in a war zone in almost every war/conflict since (two uncles served during Korea and Viet Nam).

As for the debate - it has denigrated into a insult fest from what I can see.

Thanks for asking about my son. I'll let you know when we next hear from him.

[grey_whiskers]

Thanks for the update,

(...sound of another Giant Redwood worth of paper skidding into the far end of my reading pile... :-( )

Cheers!

[trashcanbred]

What you call "explanations" are merely guesses of what happened which fit the "evidence" as humans understand the "evidence" Guesses can never be proof as any scientist worth their degree will attest.

Guesses.... all the work that Paleontologists have done is all just guesses. Just a wave of your hand simply dismisses it.

Ok have a good night.

[stultorum]

"(Most people stand on the tracks and never even hear the train coming)"

And if we elect Hillary, we won't be on the wrong side of the track; we will ON the track. HeHe!

[stultorum]

we will ON the track = we will be ON the track.

[null and void]

Hmmmm. When I read my Bible it specifically says that things were created in a certain order.

Starting with the chaos of the big bang
Moving on to the point where light came into being
Then solid matter condensed from the 'liquid' plasma.
The solids and fluids were gathered and separated
Plants came into being
Then swimming creatures
Then (dinosaurs which became) birds
Then mammals
And finally, that Johnny come lately, Man

Pretty much the same sequence that Physics and TOE have.

The main difference between the stories the Bible and Modern Science tell is the timescale. I don't know how long one of God's days is, but I do note that the Seventh Day doesn't end with "And the evening and the morning were the nth day" like days 1-6.

I assert that we are still in the Seventh Day as the Bible never says it ended...

And the Bible deals with what and why, while Modern Science deals with what and how.

[SoldierDad]

I really don't know why I keep getting accused of "dismissing" the work of all these scientists when I'm just asking questions (and not getting any answers). If I say I get that some animals have shown "evidence" of micro-changes, I'm then told I'm dismissing "evidence" by waiving my hand.