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Scientists were able to get molecular information from 1.7 million years old teeth using a new method that could completely change how we study extinct organisms.

Hosted by: Stefan Chin

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Sources:
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Images:
https://www.videoblocks.com/video/seamless-looping-animation-of-rotating-dna-strands-e1hwm_0cgiks0m37h
https://www.videoblocks.com/video/paleontologist-studying-dinosaur-fossil-tooth-from-prehistoric-time-sd5i6orozj6j9wek6
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https://www.istockphoto.com/photo/woolly-rhinoceros-gm486909394-73805857
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(Intro)

In a study published last week in Nature, scientists were able to get molecular information from teeth that are more than 1.7 million years old.  With it, they determined the sex of the animals and even found that we'd been grouping ancient rhinos incorrectly, but that's not the most exciting part.  The method may allow us to get similar data for fossils tens of times older than that, which could completely change how we study extinct organisms.

Today, when scientists want to determine the species and lineage of a creature, they usually try to sequence its DNA.  That's because genomes contain the most evolutionary information.  They literally contain all of the blueprints to build organisms, but DNA is fragile and over time, it breaks apart.  The technology to retrive DNA from ancient samples is improving, but it's just not likely that fossils which are millions of years old have enough DNA left for meaningful sequencing, so for those, pretty much all researchers have had is morphology, that is, the shape of the bones and how similar they are to others.

As you might imagine, that has its drawbacks, because looks can only tell you so much.  Just ask a paleontologist whether torosaurus is the adult form of triceratops or ask an anthropologist whether the so-called hobbit fossils from Indonesia represent a human species or a developmental disorder, but it turns out that you don't have to choose between DNA and morphology. 

There's an option in between that lets researchers get a fuller evolutionary picture while getting around that whole DNA doesn't last thing.  They can sequence the proteins instead.  Because proteins are built from DNA blueprints, they also contain what scientsist call genetic information.  It's just a bit less information than DNA because some details are lost in the translation step.  It's more information than morphology, though, so much like DNA sequences, protein sequences can be used to test evolutionary hypotheses and more accurately determine the relationships between organisms, and proteins hold up a lot longer than DNA does.  

Scientists have recovered them from 3.8 million year old eggshells and they've even detected amino acids, the building blocks of proteins, in 300 million year old fish fossils, and if you can determine the amino acid sequence for an ancient protein, you can compare that to sequences of the same protein.  That lets you perform analyses similar to what we do with DNA.

Even if you haven't sequenced proteins from other species directly, you can infer amino acid sequences from DNA data, because the genetic code which translates genes into proteins is the same for all living things, so you can build a database of proteins from genome sequences and then compare other proteins to an ancient one, but which proteins you use makes a difference. 

This actually isn't the first time scientists have gotten protein sequences from really old fossils.  A similar thing was done for structural proteins called collagens in an 80 million year old dinosaur bone, but because the genes for those proteins are widespread and similar in many species, the information wasn't super useful.  Scientists couldn't figure out whether the creature was more closely related to modern birds or modern crocodiles, and that's why, for the new study, the multi-national team tried their luck with dental enamel instead.  

They successfully extracted protein fragments from 15 teeth from a site in Dmanisi, Georgia, which was dated to almost 1.8 million years ago.  Then they sequenced them using the same approach as that ancient dino collagen, a technique called tandem mass spectrometry.  A mass spectrometer can identify molecules in a sample by bombarding them with electrons to make them charge, then sorting the charged particles by mass.

Because a molecule's mass is determined by its atomic components, scientists can use mass to identify different compounds.  Tandem mass spectrometry takes the process one step further.  The molecules go through one mass spectrometer, then get split up into smaller fragments to go through a second mass spectrometer.  That helps increase accuracy, so researchers can really reliably sequence small amounts of stuff like ancient proteins, and right off the bat, the researchers were able to figure out if the teeth were from male or female animals.

It turns out the gene for a particular version of an enamel protein is found on Y-chromosomes, so the presence of that protein indicates a tooth is from a male, but researchers were really excited by one of their samples: a lower molar which morphology suggested belonged to a member of the genus Stephanorhinus, an extinct rhinoceros from the (?~4:04).

It provided so many sequences that the team was able to construct a molecular evolutionary tree that included it, several modern rhinos, and two other extinct ones.  That confirmed the morphology was right about the ID and it helped sort out where the genus fits into the rhino family.  You see, there's been some debate about whether Stephanorhinus was an ancient relative of the Sumatran rhino or more closely related to the now-extinct Woolly rhinoceros, and the data from the tooth enamel sided with the latter.

Constructing such a robust evolutionary tree is a great proof of concept, because teeth are everywhere in the fossil record, and dental enamel contains some of the toughest proteins we know of.  That means this method could answer some of the biggest questions in paleontology, archaeology, and anthropology, like, using this technique could help us construct a better human family tree and answer questions like where did our species evolve and how exactly do we relate to other hominids?  After all, almost all of the fossils of our hominin kin, like Lucy, are beyond the reach of ancient DNA, but not ancient proteins, and protein analysis could be tried in more recent fossils where DNA extraction has failed, like the so-called hobbits of Flores, and it might even settle some long standing debates about dinosaurs, though it's a little too soon to say that definitely.  

After all, the enamel in this study was a little less than two million years old, and dinosaur fossils are more than 30 times that age, so the researchers say we can't assume the process will work on something so ancient, but as we mentioned earlier, protein sequences have been recovered from dinosaur fossils, so there's hope, and wouldn't it be great to settle that triceratops debate once and for all? 

Though, when you think about it, it's kind of amazing that we know as much as we do about long extinct animals without genetic information, and that's basically due to geometry.  By comparing shapes and measuring angles, paleontologists can make some pretty accurate guesses about what species a bone came from or how an animal moved, and if you want to understand the power of geometry for yourself, well, that's something that Brilliant.org can help you with.

Their geometry fundamentals course gives a fantastic overview of everything from basic area calculations to 3D geometry and more.  When you're done, you'll start seeing how geometry is all around us, all the time, and you'll be one step closer to studying dinosaurs, and if you sign up for a premium subscription, you'll get access to all of their courses, so you can dive deeply into all kinds of math, science, and engineering.  Plus, right now, the first 200 people to sign up at Brilliant.org/SciShow will get 20% off of their annual premium subscription, so there's never been a better time to sign up.

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