Ancient DNA -- What It Is and What It Could Be

i'ma
0:05molecular paleontologist some sophisticated
0:09actually I just made it up I spend most my time
0:12in the lab or in front of a computer but during the summer
0:15I prefer to spend my days and nights in the far north
0:19where I divide my time between waging war against mosquitoes
0:23and searching for the remains have Ice Age animals
0:26which I bring back to the lab to extract their ancient DNA
0:29as an early career scientist I was interested in ancient DNA for three
0:34reasons:
0:34first it was an opportunity to combine my interests in paleontology geology and
0:40molecular evolution
0:41I could get DNA from fossils and use this to watch species evolve
0:46through time second it was a brand new field
0:49absolutely bursting with enthusiasm and excitement
0:53a career in ancient DNA promise to be different definitely cool and
0:57hopefully useful and a third I'd really wanted to go to the Arctic
1:01so what about the Arctic is so good for DNA
1:05well it is the best place for the long-term preservation have DNA
1:09and the reason why is quite straightforward it's called
1:12and it's been called consistently for at least the last million years
1:16this period was characterized by dramatic shifts between very cold
1:20glacial intervals
1:21and much warmer interglacial periods like the one we're in today
1:24during the glacial periods or ice ages the I
1:28the sea level was a lot lower than it is today because much to the planet's water
1:31was taken up into the glaciers forming on
1:33the confidence the lower sea level exposed a massive lands that connected
1:37at the Asian and North American continents
1:39this land mass was called the India and it's where I do much of my work
1:43now crucially brings your was not glaciated
1:46during the last ice age instead it was a rich tundra grassland
1:50that was home to an equally rich diversity have ice age: plants and
1:54animals
1:54today most to the species are extinct but their bones and other hard bits
1:59tusks
1:59teeth hair sometimes even for monies survive frozen to the ground
2:03called permafrost we look for frozen bones wherever the permafrost is melting
2:09along river beds around lakes and active gold mining sites such as this one in
2:13Canada's Yukon Territory
2:14all the gold miners wash away the permafrost to get to the gold
2:18there and gravels beneath thousands have bones are unearthed
2:21over the last decades I and colleagues from around the world have extracted DNA
2:26from
2:26tens of thousands of these bounds and use them to better understand
2:30how Ice Age animals were affected by climate change in particular the last
2:35ice age
2:36we've learned for example that bison horses and ma'am it's really liked it
2:40when I was cold
2:41this is when their populations with the biggest genetic diversity
2:44the most part as a got warmer many these populations order to decline and
2:49eventually went extinct
2:50we watched brown bears during the last ice age disperse out of alaska across
2:54Asia and into europe
2:56presumably chasing after these growing populations over before us
2:59we've asked questions such as why do some species including
3:03the the cave lion go extinct while others
3:06but the caribou continue to thrive today and today we find ourselves in the
3:11middle at the gym Nomex revolution
3:13once again with growing enthusiasm to push this a little bit further
3:16we find ourselves more and more frequently being asked and asking each
3:20other
3:20can we sequence a complete genome of an extinct animal and
3:23dare we say it actually bring one back to life to answer this let me first
3:29recap very quickly when I'm going to call the seven that they describe a
3:33deeply oversimplified steps
3:35to bringing an extinct species back to life first you have to sequence the
3:38genome
3:39and somewhere in there are the jeans from its these ABC's geez antes
3:43the genes that code for the proteins that make the cells are the body's the
3:46behaviors have the things we're trying to bring back
3:48then we have to get these genomes on the chromosomes because chromosomes are the
3:53way that genetic material
3:54is carried in the cells then we have to get the chromosomes into the nucleus
3:58and the nucleus into the cell so they can start to divide and then we have to
4:01get the cell
4:03at the embryo into a surrogate mother
4:06so that it can actually grow up and develop and become something and
4:08presumably
4:09her genome isn't going to have too much to say about this developmental process
4:14and then she's got to take this developing embryo and fetus actually
4:17two-term
4:18in this case this is also not simple there's a
4:21very large size difference between the much larger mammoth
4:25and smaller elephants and it's not known whether it will actually be
4:28physically possible for female elephant to carry a baby mammoth two-term
4:33without disaster but assuming disaster is a burden the mammoth can be bored and
4:38learn how to be a mammoth we then have to find a place for to live
4:41so can go about doing mammoth the stuff and eventually make more mammoth
4:45pretty straightforward k so easy might be an exaggeration
4:50or an outright lie but let's not get caught and semantics a.m.
4:54so where are we in this with a mammoth the first attempts to sequence a
4:58complete genome a mammoth was published in 2008
5:01in the journal Nature the authors manage to sequence 3.3 billion base pairs
5:06have mammoth DNA when this was all put together in back to the elephant that
5:09look like
5:10about fifty percent have the mammoth genome had been sequenced
5:1350 percent that's about half so said if this we're working with
5:17this but that's okay that's great that was state-of-the-art in 2008 and its
5:22pretty much stay to the arts today in fact does anybody know
5:25how many vertebrate genomes have been completely sequenced including
5:30modern vertebrates living vertebrate species
5:33give you a hint it's not a very big number none
5:37not even our own genome for which an honest to goodness ridiculous amount of
5:41sequence data has been published
5:42we do not know the complete sequence of our own team
5:46I'm being a little bit unfair we do know more than 99 percent
5:49have the genome the party barge in on that actually codes for things where the
5:52jeans live
5:53the you chromatin it's the other part the heterochromatin
5:56that is made as tightly condensed repeat sequences that are just super hard to
6:00sequence through
6:02the heterochromatin doesn't make up a very big part of our genome it might not
6:05actually be that important but we don't know
6:08because we have a menace to sequence it for living thing
6:12for the mammoth we don't know the heterochromatin we also don't know where
6:15the jeans are much less
6:17where the specific genes that make a mammoth look like a mammoth
6:20are so we can find them and use that said
6:23hybridized so what we do how we fix this problem
6:27well seems pretty clear let's finish it we go into the Arctic we find a really
6:32well preserved mammoth bone we take a chunk out of it and bring it back to the
6:35lab them
6:35sequence the genome that's where the fun begins
6:38if I'm gonna sequence my own genome I could start with say a piece of my hair
6:43and I could dissolve enough in the extraction stuff
6:46and sequence everything that was in there and the results would look like
6:49this
6:50pretty much everything inside that DNA extract would be me
6:53my own DNA that's because I'm alive my DNA is in good condition
6:57left my hair has it anywhere particularly weird not so for the
7:00mammoth
7:02a similar experiment performed on a mammoth bone from alaska
7:05resulted in about 50 percent or more than half of the sequences in that tone
7:09being mammoth
7:10the other half was a combination of plants bacteria other stuff for the
7:13gotten into the bone
7:14while it was in the soil and stuff that might have been introduced into the bone
7:18during the process of excavation and sequencing we touched a boner
7:22breathe on the sample but they're still pretty good permafrost preserved more
7:25than fifty percent
7:27here's a similar experiment for a Neandertal from a cave in Croatia
7:31here only three percent have the sequences in that extract were actually
7:35primate and that includes both Neandertal sequences and any potentially
7:39contaminating
7:40human sequences but this is still good there's still
7:43the other told DNA in this sample just not much of it
7:46so presumably what that means is all we have to do is sequence a lot more of it
7:51and to some extent that's absolutely true but there is another problem
7:55you imagine that our own DNA is like a rope or a ridin or
7:59party streamers say like those were gonna put up to celebrate
8:02the birth of our first cloned mammoth the mammoth DNA itself is actually going
8:07to be
8:07more like confetti
8:11that's been run over by a part of mammoths in the rain
8:16water oxygen solar radiation bacterial decay all of these things
8:21will begin to act on the long strands to DNA immediately after an organism dies
8:27and eventually that DNA will be chopped down into smaller and smaller fragments
8:31until there's nothing left so this is what we have to make
8:35this to make the EU's and eventually that
8:40it's a hard problem its problem that probably won't be solved without
8:44new and different biotechnology than what's available today
8:48but as we progress toward this goal we're going to learn a tremendous amount
8:51about these extinct animals
8:53knowledge that I have no doubt will help us to win battles against extinction
8:57that are happening in our world today
9:00will learn where the jeans are we learned what genes make them look
9:04an act the way they did will learn a lot more about how genes interact with the
9:08environment
9:09and will finally hopefully discover why some populations
9:14and some species are so much more susceptible to extinction
9:17than others are at the same time we will get better at extracting DNA from
9:22our ancient the ancient bones we will learn how to fix the broken bits so we
9:27can start piecing together these little tiny fragments into longer and longer
9:30fragments
9:32if that's what we want to do we will eventually be able to sequence the
9:36complete genome of an extinct animal
9:38and then we will have completed step 1: thank you