Ancient penguin DNA raises doubts about accuracy of genetic dating techniques

Nov 10, 2009
Adelie penguins have survived in Antarctica for thousands of years and are invaluable for genetic research.

Penguins that died 44,000 years ago in Antarctica have provided extraordinary frozen DNA samples that challenge the accuracy of traditional genetic aging measurements, and suggest those approaches have been routinely underestimating the age of many specimens by 200 to 600 percent.

In other words, a biological specimen determined by traditional to be 100,000 years old may actually be 200,000 to 600,000 years old, researchers suggest in a new report in Trends in Genetics, a professional journal.

The findings raise doubts about the accuracy of many evolutionary rates based on conventional types of genetic analysis.

"Some earlier work based on small amounts of DNA indicated this same problem, but now we have more conclusive evidence based on the study of almost an entire ," said Dee Denver, an with the Center for Genome Research and Biocomputing at Oregon State University.

"The observations in this report appear to be fundamental and should extend to most animal species," he added. "We believe that traditional DNA dating techniques are fundamentally flawed, and that the rates of evolution are in fact much faster than conventional technologies have led us to believe."

The findings, researchers say, are primarily a challenge to the techniques used to determine the age of a sample by genetic analysis alone, rather than by other observations about fossils. In particular, they may force a widespread re-examination of determinations about when one species split off from another, if that determination was based largely on .

For years, researchers have been using their understanding of the rates of in cells to help date ancient biological samples, and in what's called "phylogenetic comparison," used that information along with to determine the dates of fossils and the history of evolution. The rates of "underpin much of modern evolutionary biology," the researchers noted in their report.

"For the genetic analysis to be accurate, however, you must have the right molecular clock rate," Denver said. "We now think that many genetic changes were happening that conventional DNA analysis did not capture. They were fairly easy to use and apply but also too indirect, and inaccurate as a result."

This conclusion, researchers said, was forced by the study of many penguin bones that were well preserved by sub-freezing temperatures in Antarctica. These penguins live in massive rookeries, have inhabited the same areas for thousands of years, and it was comparatively simple to identify bones of different ages just by digging deeper in areas where they died and their bones piled up.

For their study, the scientists used a range of mitochondrial DNA found in bones ranging from 250 years to about 44,000 years old.

"In a temperate zone when an animal dies and falls to the ground, their DNA might degrade within a year," Denver said. "In Antarctica the same remains are well-preserved for tens of thousands of years. It's a remarkable scientific resource."

A precise study of this ancient DNA was compared to the known ages of the bones, and produced results that were far different than conventional analysis would have suggested. Researchers also determined that different types of DNA sequences changed at different rates.

Aside from raising doubts about the accuracy of many specimens dated with conventional approaches, the study may give researchers tools to improve their future dating estimates, Denver said.

Source: Oregon State University (news : web)

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Yellowdart
3 / 5 (2) Nov 10, 2009
Can someone explain why it would be "underestimating" the age by 200 to 600 percent, if as Dr. Denver states the rates of evolution are much faster than previously concieved?
NotAsleep
not rated yet Nov 10, 2009
There's nothing in this article relating "DNA dating" to radiometric dating. It seems like radiometric dating would help to verify these claims...
GuruShabu
3 / 5 (2) Nov 11, 2009
I also cannot understand that point: How the DNA changing rates can be faster and one would "underestimate" the age?
It should be quite the contrary.
Something is wrong in this article...or I did not understand anything there.
LenSteenkamp
not rated yet Nov 11, 2009
Phew, I was getting seriously worried about my intelligence there for a moment. Hopefully somebody will sort this out quickly, otherwise we have the anti-evolusionists throwing massive parties!
DraganGlas
5 / 5 (2) Nov 11, 2009
Greetings,

The paper indicates that "the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons" (http://www.cell.c...0178-4).

The mitochondrial DNA "clock" runs "faster" than the phylogenetic indicators.

Since they use mitochondrial DNA changes to date specimens, on the assumption that this was the more accurate "clock", their dates under-estimate the true age by a factor of anything from two to six.

See?

[I only cleared the confusion in my own mind by reading the actual paper!]

Kindest regards,

James
GaryB
4.5 / 5 (2) Nov 11, 2009
So, to make it more clear:

They've been using a faster mitochondrial clock to "time" how fast changes take place in the phylogenetic clock because they had assumed that these clocks tick at the same rate. Thus, the phylogenetic clock is actually 200-600% slower than previously thought.

This means that the young Earth creationists will shortly be admitting they were wrong, foolish really, and will soon re-asses their theology to encompass a very old Earth, evolution and come to see Darwin as one of their intellectual heros.

(I might have mis-interpreted my second conclusion)
DraganGlas
5 / 5 (1) Nov 11, 2009
@GaryB

Correct - it's like discovering that your wristwatch is running faster than the town-hall clock.

As to the second conclusion - sadly unlikely.

Kindest regards,

James
Yellowdart
not rated yet Nov 11, 2009
Yeah, well Dr. Denver doesnt help much then, when he says

"We believe that traditional DNA dating techniques are fundamentally flawed, and that the rates of evolution are in fact much faster than conventional technologies have led us to believe."

Sounds like he's saying the wristwatch is correct and not the townclock...

From his quote in line with your quote from the paper James, it seems "greater" = "faster"

not "slower"

Kinda like having a greater decay rate would mean its "faster".

I'm only being picky, because it sounds like genetic clock testing/dating needs alot more refinement in the least.

"We now think that many genetic changes were happening that conventional DNA analysis did not capture. They were fairly easy to use and apply but also too indirect, and inaccurate as a result."

DraganGlas
5 / 5 (1) Nov 11, 2009
@Yellowdart,

Both paragraphs you quote mean that there's a lot more evolutionary changes occurring than conventional methods are detecting.

This doesn't mean that the town-hall clock's wrong.

It's only striking out the quarter-, half-, three-quarter- and hours - not the minutes and seconds.

The main problem is, as GaryB mentioned, that they thought that the rates of mitochondrial DNA and phylogenetic indicators were the same - both hourly.

Now they've discovered that the mitochondrial DNA - and different types of DNA - are "ticking" at all sorts of rates, which are faster than the phylogenetic indicators.

They've discovered that the "hours" of mitochondrial DNA are, in fact, minutes and seconds of phylogenetic "time". The wristwatch's "hours" are actually "minutes/seconds" of the town-hall clock. "Real time" (phylogenetic) is longer than the wristwatch (mitochondrial DNA) indicates.

I agree, though, that the article could have explained it more clearly.

Kindest regards,

James
Yellowdart
not rated yet Nov 12, 2009
@James:

Thanks for your response. I tried the link posted to the actual paper, but it didnt work. "Page not found" Maybe you can repost it.

My understanding was that phylogenetics is largely built upon..genes/DNA. If the molecular clocks were thought to be consistant here, but are not, then how is the "phylogenetic" clock...the "real"?

Now if as you seem to be positing that the phylogenetic is still an hour, then we have simply discovered that more change has occurred with in that hour. We did not increase it to a 2 hr period

In either case, if the rate is "faster" than previously thought, then more work is accomplished within a given period.

The issue is that we use phylogenetics to look backwards into history. So if our rate is in the "minutes/seconds" for indicators, then our history will be shorter.

This is why its confusing. What is the basis for the phylogenetic clock now if it is not based upon genetics?
DraganGlas
5 / 5 (1) Nov 12, 2009
Greetings,

I originally went to the "Trends in Genetics" site - Googled for it! - and then searched for "penguin dna": the first article, "High mitogenetic evolutionary rates and time dependency", was the correct one (http://www.cell.c...Search).

Phylogenetics also uses other methods besides DNA - morphology, etc. They use DNA for more recent organisms, as it's been difficult to find recoverable DNA from older specimens/fossils. The main problem is that the scientists didn't have enough older DNA samples to have noted this discrepancy before now.

Due to this recent find of penguin skeletons, thought to be 44,000 years old, the discrepancy has been proven - following earlier hints - which means that these could be anything from 88,000 to 264,000 years old.

They've been using the "faster" (mitochondrial DNA) clock to date specimens and now have found that it may be wrong.

Kindest regards,

James
Yellowdart
not rated yet Nov 12, 2009
@James:

Morphology is simply the study of the outward appearance, which is ultimately dependent upon its genetics.

According to the study, molecular clocks are not a good indicator of morphological change.
The Tuatara seems to exemplify this.

The abstract states that theyve determined these to be neutral time indepedent rates.

In other words, the previous clock was not a good basis for determining phylogenetics.

Until you find the factors/variables in the genes that directly translate to morphological changes, the phylogenetic tree is mostly pretty art.

The new clock rate, would say little about how old the penguin if the penguin's age is defaulted to its morphological evolution. In other words, the rate being 2 to 6 times greater, has no effect on the actual age of the penguin.

superhuman
not rated yet Nov 15, 2009
Yes, the conclusion runs contrary to intuition.

The actual dating looks like this (numbers made up):
You have two different species which differ in 50 positions. To find out when they diverged you use the clock rate which says it takes 10k years for one mutation on average and end up with 500k years.

If what they meant by the clock running faster were that it took only 2k years for one difference on average you would end up with *shorter* time to divergence.

However what they most likely mean (I don't have access to the article) is not that mutation rates are wrong but that only a fraction of mutations actually make it through to today as most are either reverted or removed during recombination. So while we see 50 differences it actually took 200 mutations to produce them. This results in divergence time underestimation by a factor of four. So the clock runs faster in that many more mutations happen during a given time then were believed to happen based on differences alone.
Yellowdart
not rated yet Nov 17, 2009
"This results in divergence time underestimation by a factor of four. So the clock runs faster in that many more mutations happen during a given time then were believed to happen based on differences alone."

Wouldnt it be an underestimation only of the mutations that have occured within a given time period? You havent adjusted the number of noticeable differences. You've only adjusted the number of mutations between differences or divergence. The given period is remaining the same, because you've assumed that the divergence is independent of the mutation rate.

If that is the case, then the mutation rate is not a determinant of how old the penguin is for instance, younger or older.

But if you've changed the divergent rate, to 4 times faster, and seeing 200 differences within what was thought to be 50...then divergence is occuring 4 times faster, than previously thought. It would make the penguin, younger..not older.
superhuman
not rated yet Nov 18, 2009
Wouldnt it be an underestimation only of the mutations that have occured within a given time period? You havent adjusted the number of noticeable differences. You've only adjusted the number of mutations between differences or divergence. The given period is remaining the same, because you've assumed that the divergence is independent of the mutation rate.

I have not assumed that divergence is independent of the mutation rate, on the contrary I said that since there were four times as many mutations since divergence it must have happened four times earlier then an estimate based on visible differences would say.

The point is that we know how long it takes for one mutation to happen on average and this is not changed, rather the article shows that the assumption that number of visible differences is equal to the number of mutations from divergence is wrong as only a fraction of those mutations remain. This in turn means that the time to divergence has been underestimated.
Tyrannical
1 / 5 (1) Dec 12, 2009
So much for all living Humans have a common ancestor from ~ 70k years ago since those calculation need to be thrown out. Wonder how much of the Recent Out of Africa theory needs to be revised.