[Felicia:] Hey, Cait. Did you hear about the time capsule the university is putting together? [Caitlin:] Time capsule? That's original. [Felicia:] What? I love the idea of a time capsule. [Felicia:] Student a thousand years from now finding the treasure trove we left them. Come on! [Caitlin:] I don't know. I'm always skeptical of these sorts of things. [Felicia:] Come on... It'll be fun. [Caitlin:] Let's submit something together. What should we put in? [Felicia:] Hair! [Caitlin:] Ugh! And we're back to my red hair again. Listen, everyone's heard everything they've ever wanted or needed -- [Felicia:] No, no, no. Let's snip off a bit of our hair and put it in a vial. That way, in 100 to 200 to even 10 000 years from now, people can sequence our DNA and learn everything else they've ever wanted to know about us. A piece of us will live on forever. [Caitlin:] You say that like it's a good thing... But okay. Maybe we should freeze our hair before we put it in the vial, though. [Felicia:] Why? [Caitlin:] Well, the first ancient genome to be sequenced was hair from permafrost found in Greenland. [Felicia:] So, the ice helps to preserve the hair then? [Caitlin:] Yup. Scientists have been able to obtain all sorts of samples from permafrost, and study ancient organisms. Not just humans, but also the woolly mammoth and influenza virus. [Felicia:] Okay. Wait here, I'm going to go to the ice machine and I'll be right back. [Caitlin:] Hurry, because there's a lot to cover about ancient DNA. This week on... [Both:] DNA Decoded! [Music] [Felicia:] Okay. Let's say it's the year 30 000, so about 20 000 years from now. Scientists far in the future have opened the university time capsule and found this piece of what was clearly from a glorious head of black hair from a woman of mystery. You're saying scientists like us will be able to extract my DNA from my hair and clone me. [Caitlin:] Well, it depends on how well the sample is preserved. DNA begins to degrade as soon as the organism dies. But since you've brought it up, let's talk a bit about Ancient DNA, the field that studies DNA from ancient specimens. The field of the Ancient DNA has been around since 1984. That's when scientists reconstructed the DNA of this guy, a quagga, an extinct species of zebra that looks like a cross between a zebra and a horse. We've sequenced the whole genome of the passenger pigeon, the woolly mammoth, and other long-extinct species. [Felicia:] I'm having a flashback to the movie Jurassic Park. Can scientists clone dinosaurs? [Caitlin:] Not likely. There's not much hope for retreiving the full genome of dinosaurs. They vanished about 65 million years ago and their DNA has long degraded. But, we might be able to bring back species like the Tasmanian tiger or even the dodo. [Felicia:] No! [Caitlin:] Yes! In the last few decades, the technology has advanced considerably. So, now it's just a matter of having the money to do it, and deciding if we want to, given the ethical challenges. But for now, let's stick with the logistics. [Felicia:] Okay. For the sake of argument, how would you bring back an extinct species? [Caitlin:] Well, first we need to find some DNA to work with. We said DNA deteriorates over time, so we won't have any luck with the dinosaurs. But we might have more luck with a species that went extinct more recently. For example -- woolly mammoths! They went extinct about 10 000 years ago. And lucky for us, their carcasses were preserved by permafrost in Siberia. [Felicia:] How about getting samples from museums? As long as you have any type of skin or muscle preserved, we should be able to get the entire genome out of it. [Caitlin:] That should work. Bones are a lot harder to use. Bones are made up mostly of minerals. They don't have as many living cells as soft tissue. [Felicia:] But teeth are an especially good source of DNA. There are two problems scientists regularly run into when they try to reconstruct a genome from fragments. The first is quality. You might not have a good sample available. So, you need to make the most of what you have. The second problem is quantity. There might not be enough genetic material in the sample to reconstruct the entire genome. [Felicia:] So, what's the difference between a good sample and a bad sample? [Caitlin:] Contamination. Did you know that for many years, scientists were convinced that we wouldn't be able to recover DNA from Egyptian mummies? They thought that the mummies' DNA would have been destroyed by the chemicals used in mummification, or by the desert heat. [Felicia:] It wasn't? [Caitlin:] No. It turns out that the problem was with the methods the researchers were using. You remember the PCR technique? Well, it's great for finding and extracting DNA fragments, but PCR can't always distinguish between ancient DNA and contamination. [Felicia:] What kind of contamination are we talking about here? [Caitlin:] Well, contamination could be from bacteria, insects, or anything else organic that found its way into the mummy's tomb. Plus, it's always possible that people who have handled the mummies have gotten their DNA mixed in with the samples. [Felicia:] So, how do scientists handle ancient DNA to prevent contamination? [Caitlin:] Well, lucky for us, we're at McMaster University, home to the Ancient DNA Centre, led by Dr. Hendrik Poinar, a world leading expert in ancient DNA. Let's take a peek into this lab... [Felicia:] Whoa! Look at all those awesome white suits. I want one! [Caitlin:] Those white jumpsuits help keep samples free of contamination while researchers are working with the ancient DNA. Okay, back to my story... Until recently, we were only able to isolate small fragments of DNA from 16 ancient Egyptian mummies. But, in 2017, a team of researchers in Germany used DNA sequencing to fish out fragments of ancient DNA from the surrounding contamination. They managed to sequence the genomes of 90 ancient Egyptian mummies. [Felicia:] Cool! But what happens when you only have fragments of DNA to work with? [Caitlin:] If you are a scientist working with DNA, you cross your fingers and hope that you'll be able to find a cell with an intact nucleus or mitochondrion. [Felicia:] Because the nucleus and the mitochondrion contain all of the organism's DNA. [Caitlin:] If you can only find fragments, then you're in for some seriously hard work. [Felicia:] But we've seen that even chopped up DNA pieces can be put back together. That's what the Human Genome Project did. [Caitlin:] Right. It can be done, but it's not easy. You know how the Human Genome Project looked for overlapping areas in the DNA? Well, you can look for overlapping areas in ancient DNA to figure out how the fragments fit together. [Felicia:] So, it sounds like it would be easier to piece the fragments together if you had a lot of samples to compare. Correct? [Caitlin:] You got it. So, if we're trying to resurrect an extinct species, it would be easier to pick a species that was once fairly common, like the woolly mammoth. [Felicia:] What about the quagga, the zebra that looks like a horse? [Caitlin:] That could work. Another technique that we haven't talked about yet is to map the fragments of ancient DNA against the DNA of the closest living relative. Mapping the DNA of an extinct zebra against living zebras would provide hints on how the fragments fit together. But, it means that you've got to make some educated guesses. [Felicia:] What do you mean? [Caitlin:] If all you've got to work with are short fragments of DNA, then there'll be some gaps in the sequence, that we may never be able to know. We can look at the closest relative for clues, but those are just guesses -- and they may not be right. Theoretically, we could manufacture genes for passenger pigeon traits and insert them into the genome of a stem cell for a common rock pigeon. But the result would be an approximation of passenger pigeons rather than an exact replica. [Felicia:] I don't even want to think about all the ways that that could actually go wrong. [Caitlin:] Exactly! That's why there are guidelines and criteria for those working in the ancient DNA field. [Felicia:] So, pros and cons... It's in our best interests to preserve biological diversity. [Caitlin:] Right. Both Britain and Russia are already working on a genetic database to preserve the genomes of endangered species. [Felicia:] And any genetic manipulation techniques that we've developed can also be used to help preserve endangered species, especially those that don't breed easily in captivity. [Caitlin:] But there's a big difference between piecing together the genome of an extinct species and restoring species. For instance, if we wanted to clone a dinosaur, we would need to know how to build an egg to house the dinosaur embryo. If we wanted to clone a woolly mammoth, we would need to insert the embryo into the womb of a surrogate mother. We could use the Asian elephant as a surrogate mother, but the Asian elephant is also an endangered species. Zoos have breeding programs for endangered species, but animals bred in captivity are rarely released into the wild, and species wouldn't be sustainable in the wild if they don't have enough genetic diversity. [Felicia:] Ancient DNA can tell us a lot about the world around us. It can be used to study the evolution of plants, animals, bacteria -- and yes, even viruses! Ancient DNA can tell us how plants like corn and bananas have changed over centuries. It can also tell us how animals like horses and dogs were domesticated. [Caitlin:] We can also use it to trace migration patterns. For instance, we know humans on other continents are descended from a single migration of Africans between 50 and 80 000 years ago. [Felicia:] It makes you wonder, what was happening around that time that caused them to leave? [Caitlin:] We can even use it to study the evolution of our natural enemies: bacteria and viruses. A good reason to study ancient DNA is that most pandemics are caused by bacteria and viruses that have been around for a long time. The Black Death killed about 50 percent of the population of Europe in the 15th century. The bacteria that caused the plague is still around. By studying the Spanish flu epidemic in 1918 that killed 50 million people, we might be able to prevent a similar disaster in the future. [Felicia:] Whoa! Black Plague and Spanish Flu. Sounds scary, doesn't it? You shouldn't have to worry though. As we've seen, this type of research happens in laboratories specifically designed to prevent contamination. Also, scientists are often only working with pieces of these pathogens, rather than the whole thing. [Caitlin:] Understanding organisms that have caused problems for humans in the past allows us to develop better treatment and prevention strategies for the future. [Felicia:] That's right. So, history doesn't repeat itself. So, even if we found a mosquito, perfectly preserved in a piece of amber, that had sucked up some dinosaur blood, we couldn't clone a velociraptor? [Caitlin:] Clever girl! Besides, too much of a liability. Come on, to make it up to you, I'll get you a white jumpsuit. [Felicia:] Deal!
