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  • More than 120 million years ago, in a hot, conifer-filled forest in what’s now India,

  • a small insect made a terrible mistake.

  • While searching for a tasty meal of pine pollen it wandered one step too far, only to find

  • itself trapped in sticky, yellow resin.

  • Tired from its flight, this small weevil was quickly entombed in the fragrant yellow material,

  • which eventually became the substance we know today as Amber.

  • Then, in 1993, scientists cracked open this very same piece of amber.

  • They took the body of the weevil, and they sampled its DNA.

  • Now, this is not a scene from the Jurassic Park franchise.

  • But this research IS from the 1990s, a decade when scientists were rushing to find the most

  • ancient DNA.

  • And at the time, this weevil was the oldest thing ever to have its DNA sampled.

  • Or, at least, so we thought.

  • The fact is, we can indeed get the DNA of extinct organisms from some fossils.

  • It’s fragmented, and it’s imperfect, but it’s possible.

  • It’s just not possible for every type of fossil, and, most importantly, not from every

  • time period.

  • It took another few decades of research, and a lot of take-backs, before scientists could

  • figure out how we could truly unlock the genetic secrets of the past.

  • The first piece of ancient DNA ever replicated was of an animal called the Quagga, a subspecies

  • of zebra that went extinct in the 19th century.

  • It was sampled in 1984, pretty much just to see if ancient DNA could be sampled at all.

  • But that research turned out to be extremely useful, and not just because it inspired Michael

  • Crichton’s famous novel.

  • The researchers used the size of differences in the DNA sequence to determine when the

  • Quagga, which is now known to be a subspecies of Plains Zebra, diverged from another species,

  • the Mountain Zebra.

  • That split happened about 3 to 4 million years ago, it turns out.

  • So even though these species of Zebras look very similar, we now know that they parted

  • ways a long time ago, before the last Ice Age began.

  • Now, that DNA was tested from a sample of dried muscle taken from a museum specimen.

  • And for the next few years, the search for ancient DNA drew from similar sourcessoft

  • tissue, preserved in things like permafrost or ice, or mummified, or trapped in amber.

  • And in the search for the oldest material, amber seemed like the best place to look.

  • After all, amber traps organisms in a perfect medium for preservation.

  • It dehydrates the DNA, which makes it more stable, and tree resin has antimicrobial properties,

  • which keeps the tissues from breaking down.

  • So, in addition to our friend the Jurassic Weevil, paleontologists sampled termites,

  • bees, and other insects from their amber tombs.

  • Not mosquitos though.

  • Amber containing mosquitoes has not been sampled for DNA yet.

  • Still, these early efforts taught us a lot about ancient DNA, and the organisms that

  • managed to hold on to it for us.

  • But there was a growing suspicion among scientists that the oldest DNA to be extracted -- including

  • the stuff from that weevil -– wasn’t what we thought it was.

  • Experts already knew that such ancient DNA wasn’t perfect or pristine.

  • Because, DNA is degrading all the time!

  • Even in living things!

  • Including you!

  • The tiny components, or base pairs, that form its code are always being changed by different

  • processes.

  • The most common of these is a process called depurination.

  • It’s caused by water molecules in your cells that attach to some of the base pairs, which

  • makes them more likely to come off.

  • Water is great for your cells, but over time, it causes damage too, including to your DNA.

  • But usually, damage like this isn’t a big deal.

  • Your cells have countermeasures that straighten, fix, or discard DNA that’s been altered

  • by things like depurination.

  • However, all those repair services go out of business ... once you die.

  • But the degradation continues.

  • Now, back in the 1990s, scientists knew all this.

  • It was part of why getting DNA from a Jurassic Weevil seemed like a miracle to some, and

  • an impossibility to others.

  • What scientists weren’t sure about was how long it took DNA to degrade to the point where

  • it was no longer readable.

  • Was it 100 years?

  • Or 100 million years?

  • Today we know that DNA has a half-life, kind of like radioactive elements do.

  • That half-life marks the amount of time until half of the DNA in a sample is degraded beyond

  • use.

  • But it can vary a lot, depending to some degree on the organism, but to even greater degree

  • on the quality of preservation.

  • For example, recent research has shown that, in cores of ocean sediments, the amount of

  • DNA from single-celled algae known as diatoms drops in half about every 15,000 years.

  • So that’s it’s half-life.

  • But, by contrast, one study of the bones of the extinct, large, flightless bird called

  • the moa, showed that its DNA had a half life of just 521 years.

  • Now, as DNA decays, it doesn’t just disappearit breaks apart into smaller, harder-to-read

  • fragments.

  • But these half-lives do mean that there’s an upper limit to how long DNA sticks around.

  • This is where preservation comes in.

  • Ideal environments for DNA preservation include colder temperatures with very limited fluctuations.

  • Closed environments are good, too.

  • DNA on the inside of bones is better preserved than DNA on the outside, because there’s

  • less interaction with the environment.

  • But even in freezing cold temperatures with best case preservation, there’s a limit.

  • A study done in 2012 of 158 well-dated fossils concluded that, even in the best circumstances,

  • DNA decays well beyond readability by 6.8 million years.

  • That’s still slow enough that readable DNA from the chloroplasts in diatoms can be found

  • in marine sediments that are up to 1.4 million years old.

  • Here at Eons, we researched this a lot, and to our knowledge,

  • that’s the oldest confirmed DNA that’s

  • ever been sequenced.

  • Yet, anyways.

  • But with new genetic techniques, scientists can read increasingly smaller chunks of DNA

  • and put them together to make longer strandslike the full genome of a 700 thousand

  • year old horse, which was sequenced in 2013 from many, many small chunks of DNA.

  • And it helps that shorter chunks of DNA, like the DNA found in your mitochondria or a diatom’s

  • chloroplast, are more stable and can last longer.

  • So if DNA becomes unreadable in less than 6.8 million years, how the heck do we have

  • DNA from a weevil that’s 120 million years old?

  • Well it turns out, thatancient weevilDNA wasn’t actually from an ancient weevil.

  • And the problem was in the methodology.

  • In order to read a DNA molecule, you need a LOT of it to make sense of what youre

  • reading.

  • This means you need to make many copies of it, in a process called amplification.

  • The easiest and most efficient way to amplify DNA is a process called PCR, or Polymerase

  • Chain Reaction.

  • PCR can quickly make even small amounts of DNA into large, consistent samples that are

  • easy to test.

  • And it’s really sensitive: All you need is an itty, bitty bit of DNA to start with.

  • But because it’s so sensitive, it can also accidentally replicate things you didn’t

  • want.

  • Like, if a single human skin cell should fall into the sample, it could be replicated so

  • quickly and thoroughly that its genetic code would overwhelm the sample.

  • And that’s exactly what happened with the sample from the weevil.

  • In the late 90s and 2000s, when lab conditions became better controlled, samples that were

  • tested in the early ‘90s were re-tested.

  • And a lot them couldn’t be reproduced successfully.

  • The DNA that we thought was from that Jurassic weevil actually turned out to be mostly from

  • a modern fungus that had gotten into the sample.

  • And the rest of the DNA was from a modern weevil, probably because the scientists were

  • comparing the old DNA to DNA from living species, and accidentally cross-contaminated.

  • Likewise, the termites and the bees preserved in Amber were all re-testedand their DNA

  • was found to be from humans, trees, fungi and other modern contaminants.

  • And when youre dealing with tiny snippets of DNA, it’s actually not that hard to mistake

  • one organism for another.

  • After all, we all share a lot of our DNA with other organisms, even ones that bear no resemblance

  • to us.

  • So if these scientists happened to pick the wrong section of DNA to replicate, they could

  • end up reproducing a section that’s in a weevil, but is also in a tree, or a human.

  • Sodoes that mean there isn’t DNA from fossils after all?

  • Nope!

  • We can get great DNA samples from some fossils, as long as theyre more recent, and most

  • importantly - if youre really careful about preventing contamination.

  • Nowadays, you have to wear a bodysuit and two pairs of latex gloves to keep your DNA

  • from falling into the mix.

  • Labs have to be sealed off from outside air, and surfaces must be bathed frequently in

  • UV light to kill any lingering genetic material.

  • And if youre comparing ancient DNA to modern DNA, you have to use two separate labs so

  • they doesn’t get mixed up.

  • But all these precautions are worth it, because when it’s amplified properly, ancient DNA

  • can reveal to us some wonderful things!

  • For example, DNA from fossil humans has shown us a lot about where different human populations

  • came from.

  • It’s demonstrated that humans, Neanderthals, and Denisovans were all probably interbreeding

  • during the last 100 to 200 thousand years.

  • And in 2014, ancient DNA also showed us that the extinct flightless Elephant bird from

  • Madagascar was most closely related to the Kiwi of New Zealand, and not Ostriches, like

  • we once thought.

  • So even though it doesn’t reach back to the days of the non-avian dinosaurs, some

  • DNA that weve sequenced is still pretty darned oldlike that 700,000 year old

  • horse from the Yukon Territory.

  • In 2013, it helped to illuminate the story of horse evolution, and showed that bone DNA

  • is better preserved in permafrost than we previously thought, possibly storing readable

  • pieces for up to a million years.

  • And recent research has changed what we know about DNA decay rates, too.

  • In 2016, scientists studying diatom DNA found that even though it decays rapidly for the

  • first hundred thousand years, the older stuff decays more slowly, and no longer follows

  • the regular half-life pattern.

  • Likewise, an analysis in 2017 found that older bones of large mammals held more DNA than

  • expected, given the half-life of DNA.

  • And other research has even shown that certain types of bone, like the dense bones of your

  • inner ear, hold more DNA and more likely to preserve DNA for longer.

  • So, all of this suggests that bigger chunks of DNA could last longer than we thought.

  • Weve learned a lot about the limitations we currently face when it comes to studying

  • the DNA of long-gone organisms.

  • And all of this adds up to the knowledge that extracting DNA from a 75 million year old

  • velociraptor is impossible.

  • At least, for now.

  • Remember: 25 years ago, it seemed impossible we’d ever have ancient DNA at all.

  • And right now, truly ancient DNAdinosaur DNAis out there, but it’s dissolved

  • into pieces.

  • It’s impossible to read using our current technology.

  • It’d be like trying to piece together an entire book that’s been chopped up into

  • individual wordsor letters.

  • But that doesn’t mean it’s always going to be impossible.

  • It just means that, at the moment, we can’t make out what that book says.

  • Maybe one day, perhaps even in our lifetimes, well find a way to crack that code.

  • But for now, the mysteries of that weevil’s genetic code remain a jigsaw puzzle of base

  • pairs that we have yet to put together.

  • Thanks for joining me!

  • And special thanks to our four eontologists, David Reed Rasmussen, Jon Ivy, Eric Lawrence,

  • and Steve.

  • Thank you so much for your support!

  • If you’d like to join them, head over to patreon.com/eons and pledge for some neat

  • n nerdy rewards.

  • Now, what do you want to know about the story of life on Earth?

  • Let us know in the comments.

  • And don’t forget to go to youtube.com/eons and subscribe!

More than 120 million years ago, in a hot, conifer-filled forest in what’s now India,

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我们可以从化石中获取DNA吗?(Can We Get DNA From Fossils?)

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    joey joey 發佈於 2021 年 05 月 03 日
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