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.

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

[Stultis]

The only reason you even need the wildly outlandish "Punctuated Equilibrium" myth in the first place is because of the striking absence of evidence in the fossil record for a slow progression of evolution over millions of years.

You clearly misunderstand punctuated equilibrium. It isn't about evolution above the species level at all. That is it's not concerned with evolutionary trends in genera, families, orders and so on that occur "over millions of years".

It's a theory about speciation, and therefore only concerns closely related organisms. Note that the current study analyzed the genomes of closely related species for evidence of punc eq.

[Ben Chad]

I cannot fully support a party that wishes to put ID into schools and I am wondering how do others out there deal with this dilemma. (Sorry if this has been asked before).

Excellent post.

[Radix]

Laughing here......

 

[ml1954]

I cannot fully support a party that wishes to put ID into schools and I am wondering how do others out there deal with this dilemma. (Sorry if this has been asked before).

I don't fully support it either for the same reason. My support is conditional. I'll never vote DIM, but I might not vote at all, or vote third party.

[Jaguarbhzrd]

You actually work in the public school system?

Hopefully you're a janitor and not a teacher.

The example he has given was just that, an off the head example that would hopefully make it easier for you to understand.

You have failed to understand in any way, and have gone off on a tangent about something else entirely, that had nothing to do with what he was trying to show.

[SoldierDad]

No, actually I was not calling you ignorant at all and I am not sure where that came from.

It came from all of the ganging up on I received on another thread from several evos who kept calling me ignorant because I didn't accept the TOE in it's entirety. I've had TOE explained in a number of college courses, so I'm not a "stranger" to the theory. I just don't accept the position that different species of animals "evolved" into some other species of animal. There is no evidence anywhere which supports this claim. That Evolution of animals takes place I can accept, although on that Micro-level you alluded to.

[SoldierDad]

The same way that the children of Sam Walton are all billionaires despite the meager profit margin at Wal-Mart.

Certainly an interesting, but unuseful, analogy. However, I've yet to find anyone who can tell me where are those fossil remains which conclusively demonstrat the micro-changes which would support the contention that one species of animal "evolved" into another completely different species.

[SoldierDad]

Your comment is very demeaning to janitors who work damned hard to help support those of us who work directly with students. The rest of you comment is simply cryptic and not understandable at all. Kinda like evos contentions that a species of animal "evolved" into a completely different species of animal.

[Jaguarbhzrd]

I just don't accept the position that different species of animals "evolved" into some other species of animal. There is no evidence anywhere which supports this claim.

I can't believe that you continue to claim that there is not evidence to support it.

We have fossils from so many different species that is is insane, and as we go lower in a geological strata, the fossils are older as well.

It is pretty simple to take those fossils, put them in proper order timiewise, then look at them physiologically, and figure out where they fit.

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.

We have plenty of lines that show just that, the horse is well established, as well as the whale, among others, lots of others.

A little studying on your part would fill in the ignorance of evolution that you show on these threads.

The evidence is there, you just have to be willing to look at it in an objective manner.

[PatrickHenry]

I just don't accept the position that different species of animals "evolved" into some other species of animal. There is no evidence anywhere which supports this claim. That Evolution of animals takes place I can accept, although on that Micro-level you alluded to.

I'm wondering if you ever looked at this, which explains the concept:
Evolution in Five Easy Steps.

When you've got the concept in mind, you might then visit some of these links:
TONS OF EVIDENCE OF EVOLUTION.

[null and void]

Fom a source other than that eeeeevil Science, and also from a totally different approach that studying the fossils you dispute.

Same conclusion, though...

[trashcanbred]

I have posted it in the past. And numerous other people have posted it over and over again as well. I gave him a link to look at.

[Coyoteman]

Your response only confirms what I posted in #135, above. You reject the theory of evolution because it goes against your religious belief, not because of any merit or lack or merit of the theory itself.

Well, a believer is someone who already believes, or has faith, in evolution. The non-belivers are the ones who need to be converted to evolution.

One particular point on your comment here; scientists do not "believe" in their theories, but rather accept those theories as long as the evidence supports them. If evidence is found to contradict a theory, it is either discarded or modified to fit both the new evidence and the old.

This definition of "theory" from my list of definitions may help you understand this point (from a google search, with additions from this thread):

Theory: a well-substantiated explanation of some aspect of the natural world; an organized system of accepted knowledge that applies in a variety of circumstances to explain a specific set of phenomena; "theories can incorporate facts and laws and tested hypotheses." Addendum: "Theories do not grow up to be laws. Theories explain laws." (Courtesy of VadeRetro.)

Theory: A scientifically testable general principle or body of principles offered to explain observed phenomena. In scientific usage, a theory is distinct from a hypothesis (or conjecture) that is proposed to explain previously observed phenomena. For a hypothesis to rise to the level of theory, it must predict the existence of new phenomena that are subsequently observed. A theory can be overturned if new phenomena are observed that directly contradict the theory. [Source]

When a scientific theory has a long history of being supported by verifiable evidence, it is appropriate to speak about "acceptance" of (not "belief" in) the theory; or we can say that we have "confidence" (not "faith") in the theory. It is the dependence on verifiable data and the capability of testing that distinguish scientific theories from matters of faith.

[balrog666]

It came from all of the ganging up on I received on another thread from several evos who kept calling me ignorant because I didn't accept the TOE in it's entirety.

Put some ice on it.

[grey_whiskers]

The amount earned per item ~ the chance any one animal's remains will be fossilized.

Multiply that factor by the total number of items sold, on the one hand, or total number of animals, on the one hand, and you get a number which is non-trivial.

However, I've yet to find anyone who can tell me where are those fossil remains which conclusively demonstrat the micro-changes which would support the contention that one species of animal "evolved" into another completely different species.

Let's start before that, OK? First we agree on a definition of species, and at least try to come up with something a practicing biologist would agree on. (Not to put one's thumbs on the scale by doing so, but scientists typically have very specific definitions in mind when using a word, which can differ considerably from that of the layman. See for example the word "force" or "potential" from either physics or engineering.)

Then decide if we can see changes of that kind across generations of living animals...

Then decide what would constitute good evidence for similar changes when seen in fossils...

Then see if there are fossils that fit the bill...

Cheers!

[ndt]

"Your comment is very demeaning to janitors who work damned hard to help support those of us who work directly with students."

I have to agree with SoldierDad on this point, any comparison with him is very demeaning to janitors.

[PatrickHenry]

Lay off SoldierDad. It's no big deal if he doesn't understand evolution. A lot of people don't, and he doesn't behave like some of them do around here. Besides, he's got a son in Iraq, and that counts for a lot.

[trashcanbred]

Well to my knowledge I did not participate in the "ganging up" on you.

You say Macro Evolution has no proof. I say Creationism has "negative proof". Why you may ask?

Let me ask a question. Why is it that the farther back in the fossil record you go, the less likely you will see any modern species? And not just for the Animal kingdom but for the Plant kingdom as well? Why?

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?

But... that isn't what the fossil record shows is it? If anything, it shows that humans were not even close to being around during the time of the Dinosaurs, right? It also shows that conifers did not exists before the Carboniferous period. It shows an exceptionally large number of animals that walked/swam/grew on this Earth a very very long time before humans (or any primates) appeared on the scene.

So why is it that we have a fossil record full of animals that no longer exist yet, we have a large number of modern day animals that only go back "so far" in the fossil record?

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. Quite the contrary, the evidence shows that over an exceptionally long period of time, different species of life came and went. And that my friend, is perhaps the best "lay man's" proof that Macro Evolution is true. It EXPLAINS what we see in the fossil record and it also makes a heck of a lot of sense as well. If you agree Micro Evolution exists in the short term, it is by no means a stretch of the imagination that Macro Evolution exists over a much longer period of time.

So if anything, there is NO proof that Creationism happened. Everyone knows this, this is why people tried to repackage it as "Intelligent Design". ID says that an "unknown" creator created us (it doesn't and will not say God did). Well that makes no sense does it? What scientific proof is there that there is an "unknown creator" that did all of this?

This is why I am most exceptionally against teaching Intelligent Design as science. Because not only is there no proof to back its claim, ALL the evidence points to the contrary.

[trashcanbred]

Oh... I did not know. Well... I tried to be as respectful as I could with my posts to him regardless.

[satchmodog9]

Moreover I believe that supporters and believers in evolution are very zealous about it, which tells me that they must have an agenda. I reason that this agenda is one that goes against the survival of Western Culture and Christianity. Were they not so zealous and anti-Christians, I may allow allow myself to be coaxed into their camp and "see the light." Until then, any theory that attempts to destroy my culture and people, I will fight them, even if there is solidity to it and not mere wind.

Supporters of ID are very zealous about their beliefs. Do they have an agenda? You reason incorrectly about creationists having the goal of destroying your religion or your culture. You can be a Christian and believe in evolution. It does not have to shake your faith in God. I have been on many digs and come across fossils. The stuff is real. I have dealt with evos who believe in God and those who spit on him. I have also run across Christians who were saintly and those who will one day burn in hell no matter what they say. People who call themselves Christians and exploit those who believe them. Don't lump evos into a category of demons or Christ bashers. A lot of them are just like you.