0:00:05.7 Sarah Crespi: This is the Science Podcast for October 6th, 2023. I’m Sarah Crespi. First up this week, staff writer Erik Stokstad. He brings not one, not two, but three stories from his beat at the intersection of ecology, natural resources, agriculture and biodiversity. We’re gonna be talking about earthworms and global poverty. Next, we have freelance producer Catherine Irving. She spoke with Love Dalén a professor of evolutionary genomics about deep time DNA. This is part of a special issue on ancient DNA, and we’re going to hear about the steps needed to push ancient DNA even further back in time, and what we might learn from these older and older genomes.
0:00:53.2 SC: First up this week, we have staff news writer Erik Stokstad, who has been very, very busy. He’s had so many interesting stories over the past two weeks that I decided to bring him on for a rundown, I guess. So. Hi, Erik.
0:01:09.2 Erik Stokstad: Hey, Sarah.
0:01:10.8 SC: Let’s just do a little background here. What is your beat?
0:01:13.4 ES: I like to think of it as the environment. Sometimes I think of it as applied ecology, the world of natural resources. In my mind, it all fits together because I’m thinking about nature and biodiversity as kind of a natural resource. I think of it not in opposition with agriculture and with material resources, but it is kind of the other side of the coin in the sense that when I write about agriculture and fisheries and aquaculture and mining, those are all things that humans do to increase our quality of life. And more often than than not, they come at the expense of nature. And yet, biodiversity is so important for enabling the healthy ecosystems, the healthy environment that allow us to farm and to fish. I’m trying to figure out in my mind how we make a decent, equitable life for everyone on the planet while not trashing it.
0:02:23.9 SC: Obviously, this is a really good lead in to your stories because they’re all going to touch on some aspect of these relationships that you’re talking about. The one that actually caught my attention last week was this. How much stuff do you need to not be abjectly poor?
0:02:40.1 ES: Six tons per person per year. But to me, it’s interesting because when you come up with a number like this, I’m always trying to figure out, well, is that a big number or is it a, is it small number and compared to what.
0:02:52.9 SC: Six tons?
0:02:53.8 ES: Six tons.
0:02:55.0 SC: Sounds large.
0:02:56.0 ES: It’s not a lot of lead, but it is a lot of feathers.
0:03:00.1 SC: Okay. Yes. Right. Yeah. And what kinds of things do they measure? What goes into that Six tons?
0:03:06.4 ES: Probably everyone listening has heard of, you’re really poor if you’re living on less than a dollar a day. But, you know, one of the scientists I talked to who studies energy and natural resources and poverty, he has a problem with that number because what does it actually tell you? Right? He and others have taken a different approach, and that approach is to try and come up with an average idea of what does it mean in terms of belongings or amount of food. They are the tangible objects that really impact your quality of life. They looked, at how people live all over the world and in more places in detail, and they came up with 15 square meters of living space or a
certain number of kilometers per year. You need to be able to travel easily to get to market, to get to your job, to get to the village, social hall, to hang out with everyone else, right? So a certain amount of transportation you need every year.
0:04:13.4 ES: Food, obviously, but also clothing, appliances, a refrigerator, a modern stove, maybe a bicycle, if not your own car. They came up with all of these definitions and what’s new in this paper, what they’re doing for the first time is saying, how much does it take in terms of raw materials for society to produce that average amount of stuff per person, per year.
0:04:40.9 SC: The material that goes into the roads that you need to bicycle on, the materials that go into the bicycle, the agricultural products that go into what you eat, all of that stuff.
0:04:50.4 ES: It’s the biomass. 0:04:51.8 SC: Yeah.
0:04:52.3 ES: It’s the fertilizer, it’s the pesticides, it’s the gravel to make the road or the asphalt to pave it, or the steel that’s required to build the railroad. They kind of looked at two numbers. One is, imagine a population of people who have nothing that we would consider necessary for a decent standard of life, and they’re in a place that has nothing just right. A vast expanse of land. Settlers of Catan, if you will. You need to build the port, you need to build the railways, and you need to build the farm equipment. They came up with some numbers that say, if you’re starting from scratch or near scratch, what does it take? It’s 43 tons per person. To build all that infrastructure.
0:05:36.5 SC: So that’s why we’re colonizing Mars, yeah, okay.
0:05:39.4 ES: And then you have to maintain it, and you have to keep growing food and keep growing cotton to make clothes. They also calculated how much does it take every year to keep people out of abject poverty?
0:05:52.4 SC: And that’s six tons.
0:05:53.7 ES: That’s six tons of stuff on average per person, per year.
0:05:57.9 SC: Okay. Now, how does that compare with richer countries, what they’re using per person?
0:06:04.4 ES: Right. So this is what’s really interesting about thinking about this number as big or small. The idea is everyone should agree that this is the bare minimum. This is the bare minimum that everyone deserves to have. Basically, one of my editors said, I don’t understand this, is this. Why is this a zero-sum game, right? Why can’t more people, why can’t other people have more? And the idea there is that there’s a… The planet only has so much gravel.
0:06:34.3 SC: There’s limits, there’s boundaries.
0:06:35.8 ES: That’s the big point. There are planetary limits.
0:06:38.8 SC: All 8 billion people get six tons of stuff. Are we going to hit a lot of planetary boundaries, I guess that’s the bigger question.
0:06:46.0 ES: And the answer is no. If everyone was using only six tons, the planet would be doing much better than it is now. And the problem is…
0:06:55.9 SC: Eric, you have to tell me how much I’m using, how many tons am I using? I need to know.
0:07:01.1 ES: The average rate in industrialized countries, thinking Germany, the United States, that’s about 70 tons of raw materials every year per person.
0:07:11.9 SC: Okay. So more than 10 times. Okay, If everybody had six tons, we’d be okay. If everyone had 70 tons, we would not be okay?
0:07:19.0 ES: The big picture here is that for everyone to have a decent standard of living, it’s going to take more stuff for the very poor and less stuff for the very rich, in order to not break the back of the planet. One hope is that we can be more efficient.
0:07:40.8 SC: Do the same with less raw material.
0:07:43.4 ES: That quality of life, transportation, moving yourself and your family, however many
miles per year, you could do that more efficiently with fewer raw materials. 0:07:54.0 SC: So there’s a hope that we could add more efficiency for everybody.
0:07:57.9 ES: And that’s not news, right? I mean, this is, this paper is just another way of looking at it. It’s counting up, weighing up all the stuff. But you could do exactly the same message with diet. You could do the same thing with energy consumption. This is the big challenge we’re facing.
0:08:16.6 SC: That’s great. Erik. This is a really fun story. I’m glad that we got to talk about it. Now. We’re gonna totally shift to another story. Again, that rose to the top. I was like, I want to cover this one too. This is about avian flu reaching the Galapagos. And you know, we’ve talked a bit about avian flu on the show before. Some countries are actually vaccinating domestic flocks because migrating birds are carrying it around, dropping by getting everybody sick. You got to do these calls, but you know, not everybody’s vaccinating and it’s traveling around the globe. And so now there’s news that this deadly avian flu has reached a Galapagos. Why is this so serious, Erik? Why is it different than reaching the UK or the US or parts of South America?
0:09:01.5 ES: You remember how I was saying, you know what I’m interested in? And partly it’s the value of nature to people because it’s amazing, because it’s inspirational. And the Galapagos, that’s one of these top places for what it is, for what it represents for science, for understanding, evolution, for Darwin’s studies there.
0:09:23.1 SC: And just giant, giant turtles. I mean.
0:09:25.3 ES: It’s a special place. Yeah. The virus is called H5N1, and this is a highly pathogenic sub-variant of that which has been spreading from Asia to Europe, to North America, now down to South America by migratory birds. That’s another real challenge here, is that there are some birds that can get infected. They don’t die, and they feel well enough. Right?
0:09:48.8 SC: They could still go thousands of kilometers.
0:09:52.5 ES: Right. They they’re feeling well enough to make these incredible migrations. Yeah. But then they spread it to the local birds. That’s been a challenge everywhere for farmers and for for wildlife managers. So the fact that avian influenza, this highly contagious and deadly form of it is now there, it’s not a surprise they were bracing for it. It’s a sad sign of the challenges we’re facing
and the challenges that the Galapagos will now face that are of course mirrored on so many continents now because of what this new strain of virus can do.
0:10:30.0 SC: The native birds are being killed by this virus, they’re seeing a lot of deaths?
0:10:34.3 ES: They’re seeing the first signs, that this is the red alert that it’s there and it’s still very early. So far they only have results from five dead birds they tested, and three were positive. That tells you the virus is there, and I mean it’s certain it’s going to keep spreading. It’s certain it’s going to a lot of birds are going to die from this and what we don’t know is how bad it will be. The Galapagos has so many species that are found nowhere else so that also raises this to a high level of concern that you’ve got the lava gull, the rarest gull in the world with only 300 or so breeding pairs found nowhere else. Of course, what’s the Galapagos are most famous for, are the finches, the 18 species of Finch, the Galapagos Finch that Darwin studied. Crucial part of the evidence for the theory of evolution through natural selection.
0:11:30.0 SC: What are researchers looking into, you know, to try to help preserve the Galapagos, protect the birds there? What can they do?
0:11:36.3 ES: Well, the first thing they’ve been doing is just trying to get a sense of how the populations are doing.
0:11:42.8 SC: So there’s observation going on is there anything they can do to prevent the spread? If they do think that it’s getting serious or it’s really spreading?
0:11:50.3 ES: Out of caution, they are closing the breeding colonies where the dead birds have been found to prevent people from spreading this. And we know that this virus can spread very easily on clothing, shoes. That was one of the real problems with poultry farms, is that people were spreading this very same virus from one farm to another. So it’s been closed for that reason. This story wasn’t something completely different from the last one. One researcher said to me, a wildlife virologist who’s been studying the impact of H5N1 the sub-variant in the Northeast of the United States. She said, we have to remember that this virus, this sub-variant came out of human agriculture. I mean, it came from how we treat and manage commercial poultry. And now it’s taking this toll on the natural world because of how we humans are growing food for ourselves. So in her mind the Galapagos is paying the price of of human agriculture. For her it says we need to think right? We need to think about how we are impacting the world the rest of the world.
0:13:07.8 SC: Yeah. When we go about our business. For sure. I think you can make the same argument for the last story that we’re going to talk about but I’ll leave that to you. I’m not going to try we’re gonna end with our friend the earthworm. This is a story about how much they contribute to agriculture. And the answer it is kind of staggering. What’s the big number here?
0:13:26.4 ES: It’s 140 million tons of food a year thanks to earthworms in farm fields. 0:13:33.4 SC: Yeah. What do they do? What do they do to give us food.
0:13:35.5 ES: Earthworms? You know they’re doing this all the time and we never we so rarely notice it. But so what earthworms do is they change the soil structure right. By burrowing through it by eating plant matter. Their poop is changing the soil in a way that makes it easier for roots to grow and easier for rain to soak in rather than to run off the surface and take soil with it. So that soil structure is really can be very much improved by earthworms in ways that benefit plants. Can I bring up the nitrogen cycle?
0:14:17.4 SC: Yeah. So yeah. How do worms help with nitrogen?
0:14:19.9 ES: They speed it up. What that means is there’s nitrogen in plants they need it to grow and when they die you need something to release that nitrogen. Now earthworms help a lot ’cause they they allow the microbes to do it much faster because earthworms are eating this dead plant material. So that helps plants grow because it makes the nitrogen available more quickly to them.
0:14:45.6 SC: And this also explains the bias here towards wheat as the primary output of the worms work. You know like soy and the other kind of legumes and beans. They have some nitrogen helpers of their own. But that’s why you can say this thing about like one slice in every loaf of bread is thanks to worms.
0:15:06.1 ES: Don’t don’t take that too seriously. Alright. It’s it’s nice when you look at your meal and you’re giving thanks to all who prepared it you include the earthworms. So cereal they looked at rice, wheat, barley, corn or maize and found six and a half percent. But that was the boost to farm yields from the presence of earthworms. And so I just did a little math on my own.
0:15:32.8 SC: Oh. You did the math on the bread. Okay.
0:15:34.5 ES: I did the math on my own and that and the researcher said well that’s probably that’s
probably not too inaccurate.
0:15:40.1 SC: All right I’ll I’ll take it bread Math.
0:15:42.8 ES: I don’t know if you want to bring up this other number of 140 million tons and how large or small that is. This was the math that the researcher did.
0:15:50.6 SC: Okay let’s hear it. Let’s hear the accurate math. [laughter]
0:15:53.8 ES: So he totaled up all the all the grain that they looked at. So that’s the rice, wheat, corn, barley and then looked at annual production figures for countries around the world. And so the benefit from the earthworms is this is so lovely right? If earthworms were a country.
0:16:14.1 SC: Yes.
0:16:14.5 ES: They’d be the fourth or fifth largest food producer.
0:16:18.5 SC: Okay. A contender for breadbasket of the world is what you’re saying. [laughter] 0:16:22.3 ES: Let’s hope they don’t get that organized Right?
0:16:25.3 SC: Yeah. Okay. So what can farmers do? What can I don’t know if I can do anything but to like make sure that worms keep up these efforts that they contribute to farming. Is there anything that farmers should do to prevent them from going away?
0:16:40.0 ES: They get something out of it of course. Right? It’s not entirely out of the of the goodness of their tiny little hearts.
0:16:46.5 SC: Delicious delicious decayed organic matter. Yeah.
0:16:49.8 ES: They’re doing their thing. So what can farmers do? The simplest thing that can help earthworms is disturb the soil less. This is a term maybe some people have heard of it no-till
agriculture. The idea is that you don’t plow the soil every time you plant. You don’t plow the soil to fight weeds. You leave the soil surfaces undisturbed as possible. And that has all sorts of advantages in terms of benefits for the plants reducing soil erosion and so forth. It also helps the earthworms make their contributions.
0:17:25.5 SC: This is my favorite part of the story. [laughter] 0:17:27.3 ES: By not killing them. Right. [laughter]
0:17:29.3 SC: Yeah. Don’t kill them. And Don’t just cut them in half. ‘Cause you’re not just doubling your worm supply when you do that. I did not know. I really did think you could cut them in half.
0:17:39.3 ES: You mentioned you were interested in that and so I did a little quick research to [laughter]
0:17:43.3 SC: Due diligence. Okay.
0:17:45.8 ES: [laughter] To be able to answer your question. And it you know it depends. It depends on the kind of earthworm. There are some kinds of earthworms that can regenerate. There are some kinds of earthworms that can’t regenerate. Some can regenerate more easily than others.
0:18:01.5 SC: Play it safe. Don’t do it.
0:18:03.8 ES: Yeah. Right. Don’t do it.
0:18:06.0 SC: This is a great story. I really appreciate you walking me through these stories this week. There are even more you know we didn’t cover your mysterious sea creature and we didn’t cover elephant trunk muscles but Everybody Can go look at those online. I will link to them from the show notes. Yeah. Thank you so much Erik.
0:18:23.1 ES: Well yeah. Yay. Science.
0:18:24.1 SC: Yay. Science. Yay. Environment agriculture biodiversity and sustainability. 0:18:32.4 ES: It’s all connected.
0:18:34.1 SC: Thank you so much Eric.
0:18:34.9 ES: Great talking again.
0:18:36.4 SC: Eric Stockstead is a staff writer for Science. You can find a host of stories that we talked about linked in our show notes at science.org/podcast. Stay tuned for freelance producer Katherine Irving and researcher Love Dalén’s discussion of just how many millennia DNA can survive.
0:19:02.3 Katherine Irving: DNA is a finicky thing. When the organism dies, it usually doesn’t last very long. It starts breaking down pretty much immediately. But sometimes, fragments of that DNA can survive, and scientists around the world are still figuring out how to use them. So this week in science, Love Dalén and his colleagues write about how these paleo-genomes could change what we thought we knew about our evolutionary history, and pick out how ecological communities respond to environmental changes. Hi, Love. Welcome to the podcast.
0:19:33.1 Love Dalén: Thank you. It’s good to meet you.
0:19:34.4 KI: Your paper discusses the progress that is being made in your field and the ability to decode ancient genomes. So what kind of allows for some of the DNA in those genomes to be preserved rather than some of it not be preserved? And why doesn’t that DNA go all the way back in the fossil record?
0:19:51.0 LD: Well, we know that DNA degrades over time, even long after the death of an organism when it’s kind of in a dry bone or similar. And the main process that degrades DNA is hydrolysis. So basically, the DNA reacts with the water. And even in dry state, there’s always a little bit of water in all samples. And so this kind of leads to a continuous degradation so that DNA follows kind of a half-life process where the fragment sizes become increasingly smaller and smaller. We do know some things that lead to DNA preservation. First of all, temperature is extremely important. As all chemical reactions, the colder it is, the slower the DNA degradation is. But we also know that ultraviolet light is bad for DNA, so darkness is good. And of course, that is as dry as possible. So cold and dark and dry is ideal conditions for DNA preservations.
0:20:46.7 KI: You write though that scientists can sometimes recover these DNA fragments that remain and they can extract genetic information. So how does one go about putting together that genome for an extinct species or an ancient species?
0:20:58.8 LD: It’s a fairly long process. I mean, you’ll your starting material is typically a tooth or bone or perhaps sediments where there is DNA directly in the sediments. So the first step of this process is trying to extract the DNA. If we take bone or tooth, for example, then the first thing you do is you try to dissolve the other components of the bone. The whole idea here is to get the DNA released into a solution and then you need to purify it. After that, you need to convert them into sequencing libraries and then you sequence that these days so that you generate many, many millions of DNA reads. And then of course, you have to assemble all these short reads into a more or less continuous genome sequence.
0:21:42.3 LD: And to do that, we use reference genomes. So for extinct species, we have to use the reference genome from a close living relative. In the case of mammoths, for example, we would use the African, or the Asian elephant reference genome. Part of the problem here is that if you take your typical mammoth genome is, or an elephant genome is about 3 billion base pairs long, the DNA is typically fragmented into 50 base per fragments. That means that you have about 60 million small pieces that you have to try to puzzle together. So it’s quite a lot of work on the computer to do this.
0:22:16.7 KI: Yeah, that’s a lot of data that you’re putting together. So the research that you’re talking about kind of explores the potential of what you call deep time paleo-genomes. So what exactly makes a paleo-genome deep time? How does it become classified that way?
0:22:31.2 LD: There’s of course no formal definition of where you would draw the line, but when you look at the literature in ancient DNA, the vast, vast majority of ancient DNA studies, are first of all on humans, but also on animals and humans, so samples that typically are less than 10,000 years old, that’s probably well over 95% of all ancient DNA studies. But there are also a number of studies that have focused on the late Pleistocene, so let’s say the last 100,000 years. But when you move beyond 100,000 years, then there are just a handful of studies that have been done on such old samples. And so that is the time period that we in the paper define as being deep time paleogenomics that is beyond 100,000 years.
0:23:13.9 KI: Why is it that most studies have focused on such recent ancient DNA as opposed to the older Pleistocene DNA?
0:23:20.8 LD: I think there are a couple of different answers to that. One is that a lot of people have focused on humans and there’s a lot of interest in their sort of archaeological community about how human society has developed. And for that, there has been so much changes happening in the last 10,000 years that makes it interesting. For that reason, because of the focus on human samples, I think is one explanation why most of the work has been done on more recent times. But perhaps an equally important one is radiocarbon dating. Radiocarbon dating is extremely powerful in estimating the age of bones and teeth, but it only works up to about 50,000 years. So any sample that is older than that, then you can’t get an accurate radiocarbon date for it. And that, of course, makes it a bit more complicated in terms of just sample availability, because if you want to work on samples that are, say, 200,000 years old, then you also need to know that they are indeed that old.
0:24:16.4 KI: And radiocarbon dating is kind of the best way to do that, and that only goes back a certain amount of time.
0:24:23.3 LD: Yeah. And then, of course, the third explanation is that the older a sample is in general, the more difficult it is to get DNA from it. If you’re moving back into half a million or a million years ago, you’re not exactly picking the low-hanging fruit of ancient DNA, are you? Much of the sort of environmental changes that are really interesting, if you’re trying to understand the processes that can be created by biodiversity we see today, they happened on the time span between 100,000 years ago and, say, two and a half million years ago.
0:24:53.1 KI: Right. What kind of has changed in the technology and in the ability of scientists to gather that data that has allowed for these older fragments of DNA to be processed more quickly and in better?
0:25:04.6 LD: There are a couple of different breakthroughs or developments that have helped this, I think. Perhaps the most important one is the revolution in DNA sequencing technology that has kept going in the over the last, say, 15 years, because many of these really old samples, they have extremely little endogenous DNA. Some of our really old mammoths, for example, they have only one or one and a half, 2% mammoth DNA, and the rest is DNA from the environment and from bacteria. And if you go back to the years 2008, 2009, 2010, it would simply have been too expensive to do a project on this. But now DNA sequencing is so cheap that it is actually possible even when the samples are really bad. So that’s, I think, the primary reason. But there have also been a number of technological developments on the actual DNA under extraction and library construction front. So there have been improvements in DNA extraction methods that have been focused on really pulling out the very short fragments from the DNA extracts. So today’s methods are better at this.
0:26:12.2 KI: So what are kind of the processes that have shaped biodiversity and why has that sort of happened in this deep time period rather than more recently?
0:26:19.7 LD: I think that the main process that has shaped biodiversity throughout much of the world, is at least in high latitude and temperate regions, are the glacial cycles. And so, Earth entered into a period of ice ages starting already two and a half million years ago, and then there’s been a long series of ice ages. These have shaped a lot of the biodiversity we see today. And in order to study that, it might actually be of interest to not only study the end of the last ice age, which happened about 10,000 years ago, but actually to study multiple glaciations. And there are a couple of features that are, I think, of particular interest. So, for example, you have an extremely long interglacial about 400,000 years ago called MIS 11. I think it would be very interesting to try to
understand how that interglacial that lasted four times longer than most other Interglacial s, how that affected biodiversity, especially in Arctic species. But there’s also a transition roughly 1 million years ago where the ice ages become longer. So before that, the ice ages are about 40,000 years old, but after a million years and going forward, almost present day, the ice ages were typically 100,000 years old.
0:27:32.2 KI: Interesting. And so these glacial periods, they, is it mostly a temperature thing that’s causing these sort of changes in diversity particularly?
0:27:40.5 LD: I think it’s primarily the temperature. Of course, one needs to remember that cold adapted Arctic species, for example, they will have been expanding their ranges during glaciations. They had a much larger range during the last ice age, and presumably during previous ice ages. Whereas temperate species such as red foxes or red deer, they will have contracted into future during ice ages and only expanded during these much shorter 10,000 year long warm periods. So there is this kind of dance, if you wish, between the Arctic and the temperate species where one is expanding, the other one is contracting and vice versa.
0:28:16.7 KI: Got it. And that’s something that we’re kind of seeing today as well. You’re talking about a little bit the Arctic foxes and the red foxes.
0:28:23.3 LD: Absolutely. I did my PhD on Arctic fox genetics, so I’m quite familiar with those. But yeah, I mean, today what we see is that their range is contracting because the red foxes are expanding their range and red foxes will outcompete Arctic foxes. They are about twice as large.
0:28:37.1 KI: So you’re talking a little bit about this potential for ancient DNA to help with understanding this biodiversity shift that’s happening over these glacial periods. Why are Paleo- genomes so integral to understanding that and what is what you’re hoping that you’ll be able to do with this new ability to look at these ancient genes.
0:28:55.5 LD: Paleo-genomes are a bit like using a time machine that gives you the opportunity to actually go back in time and sample DNA at different points in time. So you can create these kind of genomic transects that span interesting time periods. That is in many ways a much more powerful way to study evolution than only relying on modern genomic data, because then you have to use inference to try to model what happened in the past. With ancient DNA you can go back and you can measure exactly what happened. With modern DNA and inference you can’t see if there was a whole clade or a whole lineage that went extinct.
0:29:31.7 KI: Interesting. So it’s kind of resurrecting lineages that we wouldn’t have known about otherwise through the models that we have.
0:29:37.6 LD: Exactly.
0:29:38.5 KI: What are some of the things that have come out of this recently? I know you mentioned in the paper there was a study about Brown bears and how they are hybrids or that this mesh of these other species, what are kind of the most fascinating things that you see have the potential to be worked on with these?
0:29:55.1 LD: Yeah, I think one of the main things that we are seeing in ancient DNA in general, but perhaps even more so when we go even further back in time, is how important hybridization has been for the evolutionary process. Everyone is familiar with the fact that most humans, at least humans outside Africa, carry a small percentage of Neanderthal DNA, and many populations also carry Denisovan DNA. But we now also know, for example, that brown bears carry DNA both from
polar bears, from an ancient hybridization, and from cave bears. So about between 2% and 4% though of the brown bears DNA is actually cave bear DNA. And in a study we did and published a couple of years ago on mammoths, we could also show that the Colombian mammoth, the North American Colombian mammoth, actually is a hybrid between, on the one hand, Woolly mammoths, and on the other hand, that previously unknown type of mammoth that we call Castocca.
0:30:49.5 KI: It makes it then a lot more complicated than just these branches of the cladogram where you’ve got all these different species sort of separate. They all will end up mixing.
0:30:58.9 LD: It’s increasingly so that instead of this classical view of evolution where everything is branching into a sort of a tree-like structure, it looks more and more like we have a weave of different lineages that disappear, that coalesce together, that merge, where there’s gene flow between lineages and so on. So I think evolution and life is turning out to be a bit more complicated perhaps than the traditional view.
0:31:25.7 KI: Exactly. You also mentioned in the paper that there are still some challenges to bringing this Glycogen DNA to the mainstream. What I guess are you and other scientists working on to make these Paleo-genomes more useful and more accessible and enabling more science to happen with this data?
0:31:40.8 LD: Well, we think that there’s still quite a lot of scope to improve the lab methods, both in DNA extraction methods that are more efficient and as well the library construction methods. There are previous studies that show that you lose quite a large percentage of the DNA during this process. That’s one area where there is definitely scope for improvement. The second area, I think, is also in the bioinformatics. So in the actual data analysis, because as the DNA fragments get shorter and shorter, they’re also more difficult to map to the reference genome and you get lots of various biases that could lead to erroneous results. So there’s definitely a lot of work that needs to be done on extremely degraded DNA fragments and how we deal with those bioinformatically.
0:32:25.9 KI: It sounds like you’ve got some exciting stuff ahead. Thank you so much for coming on the podcast, today.
0:32:30.3 LD: Thank you. I enjoyed this. This was fun.
0:32:32.3 KI: Love Dalén is an evolutionary geneticist at Stockholm University. You can find a link
to the review we discussed at science.org/podcast.
0:32:43.0 SC: And that concludes this edition of the Science Podcast. If you have any comments or suggestions, write to us at sciencepodcasts.aaas.org. Or if you’re particularly happy with this week’s show, go write us a review on your podcast app of choice. To find us on those apps, search for Science Magazine. You can listen to the show on our website, of course, science.org/podcast. The show is edited by me, Sarah Crespi, and Kevin McLean with production help from Podigy. Jeffrey Cook composed the music. On behalf of Science and its publisher, AAAS, thanks for joining us.
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