Genetic evidence for punctuated equilibrium

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.

I don't know what you believe, and I don't care what you believe. You can believe an any religion's creation story to your heart's content. Christian, Norse, Hindu, Lakota, whatever you want to believe, have at it. Just stop mischaracterizing actual science, ok?

When you say you "have yet to see" any evidence of transitional species (which is a fairly misleading term, but we'll avoid another semantic debate for now) I assume you haven't bothered to look, or you've shut your eyes any time you're in the same room as a the evidence.

In either event, let's put that issue to bed:

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

http://www.talkorigins.org/indexcc/CC/CC200.html

http://www.talkorigins.org/faqs/faq-transitional.html

PART 1 1. Introduction What is a transitional fossil? The term "transitional fossil" is used at least two different ways on talk.origins, often leading to muddled and stalemated arguments. I call these two meanings the "general lineage" and the "species-to-species transition": "General lineage": This is a sequence of similar genera or families, linking an older group to a very different younger group. Each step in the sequence consists of some fossils that represent a certain genus or family, and the whole sequence often covers a span of tens of millions of years. A lineage like this shows obvious morphological intermediates for every major structural change, and the fossils occur roughly (but often not exactly) in the expected order. Usually there are still gaps between each of the groups -- few or none of the speciation events are preserved. Sometimes the individual specimens are not thought to be directly ancestral to the next-youngest fossils (i.e., they may be "cousins" or "uncles" rather than "parents"). However, they are assumed assumed? to be closely related to the actual ancestor, since they have intermediate morphology compared to the next-oldest and next-youngest "links". The major point of these general lineages is that animals with intermediate morphology existed at the appropriate times, and thus that the transitions from the proposed ancestors are fully plausible.plausible? General lineages are known for almost all modern groups of vertebrates, and make up the bulk of this FAQ. "Species-to-species transition": This is a set of numerous individual fossils that show a change show me those fossils between one species and another. It's a very fine-grained sequence documenting the actual speciation event, usually covering less than a million years. These species-to-species transitions are unmistakable when they are found. I have not yet been shown them - just HEARD about them Throughout successive strata you see the population averages of teeth, feet, vertebrae, etc., changing from what is typical of the first species to what is typical of the next species of course there could be no other possible explanation for similarity of teeth, feet, vertabrae, etc. Sometimes, these sequences occur only in a limited geographic area (the place where the speciation actually occurred), with analyses from any other area showing an apparently "sudden" change. could explain the idea of Creation Other times, though, the transition can be seen over a very wide geological area. Many "species-to-species transitions" are known, mostly for marine invertebrates and recent mammals (both those groups tend to have good fossil records), though they are not as abundant as the general lineages (see below for why this is so). Part 2 lists numerous species-to-species transitions from the mammals. Transitions to New Higher Taxa As you'll see no, I don't "see" the transitions - just reading that they exist throughout this FAQ, both types of transitions often result in a new "higher taxon" (a new genus, family, order, etc.) from a species belonging to a different, older taxon. There is nothing magical about this. The first members of the new group are not bizarre, chimeric animals; they are simply a new, slightly different species, barely different from the parent species. Eventually they give rise to a more different species, which in turn gives rise to a still more different species, and so on, until the descendents are radically different from the original parent stock. For example, the Order Perissodactyla (horses, etc.) and the Order Cetacea (whales) can both be traced back to early Eocene animals that looked only marginally different from each other, and didn't look at all like horses or whales. (They looked rather like small, dumb foxes with raccoon-like feet and simple teeth.)and where are those fossils in between that has led to the "discovery" that whales and horses came from something that looked like a fox or raccoon? But over the following tens of millions of years, the descendents of those animals became more and more different, and now we call them two different orders.

Not exactly the convincing evidence that was "promised". Terms such as assumed and plausable don't strike much faith in the evidence as being definitive.

As I said, that article presents a good starting place. It is, however, apparent that you read very little of it.

It is equally apparent that you either (1) have some sort of handicap that prevents you from investigating anything on your own or (2) are too bloody lazy to look. I can think of no other explanations for your strangely juvenile demand to "show me those fossils" and your petulant complaint that "I have not yet been shown them - just HEARD about them."

Now, I'm going to suggest something radical here. Instead of responding to this and future posts with some variation of your happy refrain that "if them there scientists ain't got everything, they ain't got nothing," pick a specific set of transitionals identified in the link provided, and frame some alternative explanations for their existence that takes into account their age, taxonomic hierarchy, and morphological similarities and dissimilarities.

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