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1:21

This is the Science Podcast for October 6, 2023.

1:24

I'm Sarah Crespi. First

1:26

up this week, staff writer Eric Stocks said

1:29

he brings not one, not two, but

1:31

three stories from his beak at the

1:33

intersection of ecology, natural

1:35

resources, agriculture and

1:38

biodiversity. We're going to be talking

1:40

about earthworms and global poverty.

1:43

Next we have freelance producer Catherine Irving. She

1:45

spoke with Luvee Dahlin, a professor of evolutionary

1:47

genomics,

1:49

about deep time DNA. This

1:51

is part of a special issue on ancient

1:53

DNA. And we're going to hear about the steps

1:55

needed to push ancient DNA

1:58

even further back in time.

1:59

And what we might learn from these older

2:02

and older genomes.

2:08

First up this week, we have staff news writer

2:11

Eric Stockstead, who has been very,

2:13

very busy. He's

2:16

had so many interesting stories over

2:18

the past two weeks that I decided to bring

2:20

him on for like a rundown, I

2:22

guess.

2:23

So hi, Eric. Hey, Sarah.

2:26

Let's just do a little background here. What is your beat?

2:28

I like to think of it as the environment.

2:31

Sometimes I think of it as applied

2:33

ecology, the world

2:36

of natural resources. In

2:39

my mind, it all fits together because I'm

2:41

thinking about nature

2:44

and biodiversity as kind

2:46

of a natural resource. I think of it not

2:49

in opposition with agriculture

2:52

and with material resources,

2:54

but it is kind of the

2:57

other side of the coin in the sense

2:59

that when I write about agriculture

3:02

and fisheries and aquaculture

3:04

and mining, those

3:06

are all things that humans do to

3:09

increase our quality of

3:11

life. And more

3:14

often than not, they come

3:16

at the expense of nature. And

3:18

yet biodiversity is

3:20

so important for enabling the

3:22

healthy ecosystems, the healthy environment

3:25

that allow us to farm

3:27

and to fish. I'm

3:30

trying to figure out in my mind how

3:32

we make a decent, equitable

3:35

life for everyone on the planet while not

3:37

trashing it.

3:39

Obviously, this is a really good lead in to your

3:41

stories because they're all going to touch

3:43

on some aspect of these relationships that

3:45

you're talking about. The one actually caught

3:48

my attention last week was this,

3:50

how much stuff do you need to

3:52

not be abjectly

3:53

poor?

3:55

Six tons per person

3:57

per year. But to me, it's interesting.

4:00

because when you come up with a number like this, I'm

4:02

almost trying to figure out, well, is that a big number

4:05

or is it a small number? And compared

4:07

to what? Six tons. Six

4:09

tons. Sounds large. It's

4:11

not a lot of lead, but it is a lot

4:13

of feathers. Okay, yes.

4:15

Right, yeah. And what

4:18

kinds of things do they measure? What goes into that

4:20

six tons?

4:21

Probably everyone listening has

4:24

heard of. You're really poor

4:26

if you're living on less

4:28

than a dollar a day. But

4:30

you know, one of the scientists I talked to who studies

4:33

energy and natural resources and poverty,

4:36

he has a problem with that number because

4:39

what does it actually tell you, right? He

4:41

and others have taken a different approach.

4:44

And that approach is to try and come up with,

4:47

come up with an average idea of

4:49

what does it mean in terms of

4:51

belongings or amount of food.

4:54

They are the tangible objects that really

4:57

impacts your quality of

4:59

life. They looked at how

5:01

people live all over the world and in more

5:03

places in detail. And they came up

5:06

with 15 square meters

5:08

of living space or a certain

5:11

number of kilometers per year.

5:13

You need to be able to travel easily

5:16

to get to market, to get to your job, to

5:19

get to the village social

5:21

hall, to hang out with everyone

5:24

else, right? So certain amount of transportation

5:26

you need every year. Food

5:29

obviously, but also clothing, appliances,

5:32

a refrigerator, a modern stove,

5:35

maybe a bicycle, if not your own car.

5:38

They came up with all of these definitions

5:41

and what's new in this paper, what

5:43

they're doing for the first time is saying, how

5:46

much does it take in terms

5:48

of raw materials for

5:51

a society to produce that

5:53

average amount of stuff per person per

5:55

year.

5:56

The material that goes into the roads that you

5:58

need to bicycle on.

5:59

materials that go into the bicycle, the

6:02

agricultural products that go into what you eat,

6:04

all of that stuff. It's the biomass.

6:07

It's the fertilizer. It's the pesticides.

6:10

It's the gravel to make the road of the asphalt,

6:13

the pavement, or the steel that's required

6:15

to build the railroad. They kind of looked

6:17

at two numbers. One is, imagine

6:19

a population of people who have

6:21

nothing that we would consider necessary

6:24

for an decent standard of life. And they're in a

6:26

place that has nothing, just

6:28

a vast expanse of land. Settlers

6:32

of Catan, if you will, you need

6:34

to build the port. You need to build the

6:36

railways, and you need to build the

6:39

farm equipment. They

6:41

came up with some numbers that say, if you're starting

6:43

from scratch or near scratch, what

6:46

does it take? It's 43

6:48

tons per person to

6:50

build out of that infrastructure. So that's what we're

6:52

colonizing Mars. Yeah. Okay. And

6:55

then you have to maintain it, and you have

6:57

to keep growing food and keep growing

6:59

cotton to make clothes. They

7:01

also calculated how much does it take every year

7:04

to keep people out

7:06

of agit-argery.

7:07

And that's six tons.

7:09

That's six tons of stuff on average

7:11

per person per year. Okay.

7:13

Now, how does that compare with

7:15

richer countries, what they're

7:17

using per person? Right. So

7:20

this is what's really interesting about thinking

7:22

about this number as big or small.

7:25

The idea is everyone should

7:27

agree that this is the

7:30

bare minimum. This is the bare minimum

7:32

that everyone deserves to have.

7:34

Basically, one of my editors said, I don't understand

7:37

this. Why is this a zero-sum game?

7:39

Right? Yeah. Why can't more people, why

7:41

can't other people have more? And

7:43

the idea there is that there's

7:46

a, the planet only has

7:48

so much gravel. There's limits. There's

7:50

boundaries. That's the big point. There

7:52

are planetary limits.

7:54

All eight billion people get

7:56

six tons of stuff. Are we going to hit a

7:58

lot of planetary boundaries? I guess it's.

7:59

So it's the bigger question. And the answer

8:02

is no. If everyone

8:04

was using only six tons,

8:07

the planet would be doing much better

8:09

than it is now. And the problem is. Eric,

8:11

you have to tell me how much I'm using. How many

8:13

tons am

8:14

I using? I need to know.

8:16

The average right in industrialized countries,

8:18

thinking Germany, the United

8:21

States, that's about 70 tons

8:23

of raw materials every

8:26

year per person. Okay. So

8:27

more than 10 times.

8:29

Okay. If everybody had six tons, it would be okay.

8:31

If everyone had 70 tons, it would not be

8:33

okay.

8:34

The big picture here is that for

8:37

everyone to have a decent

8:40

standard of living, it's going to take

8:42

more stuff for the very

8:44

poor and less stuff

8:47

for the very rich in order

8:50

to not break the back of the planet.

8:53

One hope is that we can be more

8:55

efficient. Do the same with less raw

8:57

material. That quality

8:59

of life, transportation, moving

9:02

yourself and your family, however many miles

9:04

per year, you could do that more

9:07

efficiently with fewer raw materials.

9:09

So there's a hope that we could add

9:11

more efficiency for everybody. And that's

9:13

not news, right? I mean, this is, this

9:16

paper is just another way of looking at

9:18

it. It's counting up, weighing up

9:21

all the stuff, but you could do exactly

9:23

the same message with diet.

9:26

You could do the same thing with energy

9:28

consumption. This is the big challenge

9:31

we're facing. That's

9:32

great, Eric. This is a really fun story. I'm glad

9:34

that we got to talk about it. Now we're

9:36

going to totally shift to another

9:39

story again that rose to the top. I was like, I want

9:41

to cover this one too. This is about

9:43

avian flu reaching the Galapagos.

9:46

And, you know, we've talked a bit about avian flu

9:49

on the show before. Some countries are actually

9:51

vaccinating domestic flocks because migrating

9:54

birds are carrying it around, dropping by,

9:56

getting everybody sick. You got to do these calls,

9:58

but, you know, not everybody.

12:00

positive. That tells you the virus

12:02

is there and I mean it's

12:04

certain it's going to keep spreading. It's

12:07

certain it's going to, a lot of birds are going to die

12:09

from this and what we don't know is

12:11

how bad it will be. The Galapagos

12:14

has so many species that are found

12:16

nowhere else. So that also

12:18

raises this to a high level of

12:21

concern that you've got the lava gull,

12:24

the rarest gull in the world with only 300

12:26

or so breeding hosts found nowhere

12:28

else. Of course what the

12:31

Galapagos are most famous for are

12:33

the finches. The 18

12:36

species of finch, the Galapagos finch,

12:38

the Darwin study, crucial

12:41

part of the evidence for the theory

12:43

of evolution through natural selection.

12:45

What are researchers looking into

12:47

to try to help preserve the Galapagos,

12:49

protect the birds there? What can they do? Well the

12:52

first thing they've been doing is just

12:54

trying to get a sense of

12:55

how the populations are doing.

12:58

So

12:58

there's observation going on, is there anything they

13:00

can do to prevent the spread if they

13:02

do think that it's getting serious or it's

13:04

really spreading?

13:05

Out of caution they are closing

13:08

the breeding colonies where

13:10

the dead birds have been found to prevent

13:13

people from spreading this and we know that

13:16

this virus can spread very easily

13:18

on clothing, shoes. That

13:21

was one of the real problems with

13:24

poultry feeders, is that people

13:26

were spreading this very same virus from

13:28

one farm to another. So

13:31

it's been closed for that reason. This

13:33

story wasn't something completely different from

13:35

the last one. One researcher

13:37

said to me, a wildlife virologist

13:41

who's

13:41

been studying the impact of H5N1,

13:43

the sub-variant in the northeast of

13:45

the United States, she said we

13:48

have to remember that this virus,

13:50

this sub-variant came out of

13:52

human agriculture. I mean it came

13:55

from how we treat and

13:57

manage commercial poultry.

13:59

And

14:01

now it's taking this tool on

14:03

the natural world because of how

14:05

we humans are growing

14:08

food for ourselves. So in her mind,

14:11

the Galapagos is paying

14:13

the price of human agriculture.

14:16

For her, it says we need to think, right?

14:18

We need to think about how we are impacting

14:21

the world, the rest of the world. Yeah.

14:22

When we go about our business, for sure.

14:25

I think you can make the same argument for

14:27

the last story that we're going to talk about, but I'll leave

14:29

that to you. I'm not going to try. We're going to end

14:31

with our friend, the earthworm. This is a story

14:34

about how much they contribute to

14:36

agriculture. And the answer is

14:38

kind of staggering. What's the big

14:40

number here? It's 140 million

14:43

tons of food a year, thanks

14:46

to earthworms in farm fields. Yeah.

14:48

What do they do? What do they do to give us food? Earthworms,

14:51

you

14:52

know, they're doing this all the time and we

14:54

never, we so rarely

14:57

notice it, but so what earthworms do

15:00

is they change the soil structure,

15:02

right? By burrowing through it, by eating plant

15:04

matter, their poop

15:07

is changing the soil

15:09

in a way that makes it easier for

15:12

roots to grow, easier

15:14

for rain to soak

15:17

in rather than to run off the surface

15:19

and take soil with it. So

15:21

that soil structure is

15:23

really can be very much improved

15:26

by earthworms in ways that benefit

15:28

plants. Can I bring up the nitrogen

15:30

cycle? Yeah. So yeah,

15:32

how do worms help with nitrogen?

15:35

They speed it up. What that means is

15:37

there's nitrogen in these. They

15:40

need it to grow. And when they die,

15:42

you need something to

15:45

release that nitrogen. Now earthworms

15:47

help a lot because they allow the microbes

15:50

to do it much faster because earthworms are

15:52

eating this dead plant material. So

15:54

that helps plants grow

15:57

because it makes the nitrogen available

15:59

more quickly. to them.

16:01

And this also explains the bias

16:03

here towards wheat as the

16:05

primary output of

16:07

the worms work, you know, like soy

16:10

and other kind of legumes and beans, they have

16:12

some nitrogen helpers of their

16:14

own. But that's why you can say this thing

16:16

about like one slice in every

16:19

loaf of bread, thanks to

16:20

worm. Don't take

16:22

that too seriously. All

16:25

right, it's nice when you look

16:27

at your meal and you're giving thanks

16:30

to all who prepared it, you include the earthworms.

16:33

So cereal, they looked at rice,

16:35

wheat, barley, corn or maize

16:38

and found six and a half percent

16:41

that that was the boost to farm yields

16:43

from the presence of earthworms. And

16:46

so I just did a little math on my own. Oh, you

16:48

did the math on the bread. Okay, I did the math

16:50

on my own. And the researcher said, well,

16:53

that's probably not too inaccurate.

16:55

All right, I'll take it. Bread math. I

16:58

don't know if you want to bring up this other number of 140

17:00

million tons and how large

17:03

or small it is. This was the math that the researcher

17:05

did. Okay, let's hear it. Let's hear the

17:07

accurate math. So she

17:10

totaled up all the

17:12

grain that they looked at. So that's the rice,

17:15

wheat, corn, barley,

17:18

and then looked at annual

17:20

production figures for countries around the world.

17:23

And so the benefit from the earthworms

17:25

is so lovely, right?

17:27

If earthworms were a country, they'd

17:30

be the fourth or fifth largest

17:33

food producer. Okay, a contender

17:35

for breadbasket of the world. That's what you're saying. Let's

17:38

hope they don't get that organized, right?

17:39

Yeah, okay. So what

17:42

can farmers do? What can,

17:45

I don't know if I can do anything, but to make sure

17:47

that worms keep up these efforts that they

17:49

contribute to farming, is there anything that farmers

17:52

should do to prevent them from going away?

17:55

They get something out of it, of course, right?

17:57

It's not entirely out of the goodness of it.

17:59

their

18:00

tiny little hearts.

18:01

Delicious, delicious

18:03

decayed organic matter. Yeah. They're

18:05

doing their thing. So what can farmers

18:07

do? The simplest thing

18:10

that can help earthworms is

18:12

to disturb the soil less. This

18:15

is a term maybe some people have heard of it, no-till

18:18

agriculture. The idea is that

18:20

you don't plow the soil every

18:22

time you plant. You don't plow the soil

18:25

to fight weeds. You leave the

18:27

soil surface as undisturbed as possible.

18:30

And that has all sorts of advantages in terms

18:33

of benefits for the plants, reducing soil

18:35

erosion and so forth. It also helps

18:38

the earthworms make their contributions.

18:40

This is my favorite part of the story. By

18:43

not killing them, right?

18:44

Yeah, don't kill them and don't

18:47

just cut them in half because you're not just doubling

18:49

your worm supply

18:50

when you do that. I did not know.

18:52

I really did think you could cut them in half. You

18:55

mentioned you were interested in that. And so I did

18:57

a little quick research to be able

19:01

to answer your question. And

19:04

it depends. It depends on

19:06

the kind of earthworm. There are some

19:08

kinds of earthworms that can regenerate. There

19:11

are some kinds of earthworms that can't regenerate.

19:13

Some can regenerate more easily

19:16

than others. Play it safe. Don't

19:18

do it. Yeah, right. Don't

19:20

do it. This

19:21

is a great story. I really appreciate

19:23

you walking me through these stories this week.

19:26

There are even more. We didn't cover

19:28

your mysterious sea creature and we didn't cover

19:30

elephant trunk muscles. But

19:32

everybody can go look at those online. I will

19:35

link to them from the show notes. Yeah,

19:37

thank you so much, Eric.

19:38

Well, yeah. Yay science.

19:40

Yay science. Yay environment,

19:43

agriculture, biodiversity and

19:46

sustainability. It's all

19:48

connected. Yeah, thank you so much, Eric.

19:50

Great talking again.

19:51

Eric Stocksett is a staff writer for science.

19:54

You can find a host of stories that

19:56

we talked about linked in our show notes

19:58

at science.org slash podcast.

20:00

Stay tuned for freelance producer Taftman

20:02

Irving and researcher Luve Dallin's

20:05

discussion of just how many millennia

20:07

DNA can survive. DNA

20:18

is a finicky thing. When the organism dies,

20:20

it usually doesn't last very long. It

20:23

starts breaking down pretty much immediately.

20:26

But sometimes fragments of that DNA can survive,

20:28

and scientists around the world are still figuring

20:31

out how to use them. So this week

20:33

in science, Luve Dallin and his colleagues

20:35

write about how these paleo genomes could

20:37

change what we thought we knew about our evolutionary

20:40

history, and pick out how ecological

20:42

communities respond to environmental

20:44

changes. Hi Luve, welcome

20:47

to the podcast.

20:48

Thank you, it's good to meet you. Your paper discusses

20:50

the progress that is being made in

20:53

your field and the ability to decode

20:55

ancient genomes. So what kind

20:57

of allows for some of the DNA in those genomes

20:59

to be preserved rather than some of

21:01

it not be preserved? And why doesn't that

21:04

DNA go all the way back in the fossil

21:05

record? Well, we know that DNA degrades

21:08

over time, even long after

21:10

the death of an organism when it's kind of in

21:12

a dry bone or similar.

21:15

And the main process that degrades

21:18

DNA is hydrolysis. So basically, the

21:20

DNA reacts to the water. Even

21:22

in dry state, there's always a little bit of water

21:24

in all samples. And so this kind of leads

21:27

to a continuous degradation

21:29

so that DNA follows kind of a half-life

21:32

process where the fragment size has become increasingly

21:34

smaller and smaller. We do know

21:37

some things that lead to DNA

21:39

preservation. First of all, temperature is

21:41

extremely important as all chemical

21:43

reactions, the colder it is, the

21:45

slower DNA degradation is. We

21:48

also know that ultraviolet light is bad

21:50

for DNA, so darkness is good.

21:53

And of course, that is as dry as possible. So

21:56

cold and dark and dry is

21:58

ideal

21:59

condition.

21:59

for DNA preservation.

22:01

You're right though that scientists can sometimes

22:04

recover these DNA fragments that

22:06

remain, and they can extract genetic information.

22:09

So how does one go about putting together that genome

22:10

for an extinct species or an ancient

22:13

species? It's a fairly long process.

22:15

I mean, your starting material is

22:17

typically a tooth or bone or

22:20

perhaps sediments where there is DNA

22:22

directly in the sediments. So the

22:24

first step of this process is trying

22:26

to extract the DNA. We take bone or tooth,

22:29

for example, then the first thing you

22:31

do is you try to dissolve the other

22:33

components of the bone. The

22:35

whole idea here is to get the DNA released

22:38

into a solution, and then you need to purify

22:40

it. After that, you need to convert them

22:42

into sequencing libraries, and then you

22:45

sequence that these days so that you

22:47

generate many, many millions of DNA

22:49

reads. And then, of course, you have to

22:52

assemble all these short reads into a

22:54

more or less continuous genome sequence.

22:57

And to do that, we use reference genomes. So

23:00

for extinct species, we have to use the reference

23:02

genome from a close

23:05

living relative. In the case of mammoths,

23:07

for example, we would use the

23:10

African or the Asian elephant reference genome.

23:12

Part of the problem here is that if you take

23:14

your typical mammoth genome, or

23:17

an elephant genome, it's about 3 billion base pairs

23:19

long. The DNA is typically

23:21

fragmented into 50 base pair

23:23

fragments. That means that you have about 60 million

23:26

small pieces that you have to try to puzzle together.

23:28

So it's quite a lot of work on the computer

23:31

to do this. Yeah, that's a lot of data

23:33

that you're putting together. So

23:35

the research that you're talking about kind

23:37

of explores the potential of what you call deep

23:39

time paleo

23:40

genomes.

23:41

So what exactly makes a paleo genome

23:43

deep

23:44

time? How does it become classified that

23:46

way? There's, of course, no formal

23:48

definition of where you would draw the line.

23:50

But when you look at the literature in

23:52

ancient DNA, the vast, vast majority

23:55

of ancient DNA studies are, first of all,

23:57

in humans, but also on animals

23:59

and humans. of samples that typically

24:01

are less than 10,000 years old. That's

24:03

probably well over 95% of all

24:06

ancient DNA studies. But there are also

24:08

a number of studies that have focused on the late Pleistocene,

24:10

so let's say the last 100,000 years. But

24:13

when you move beyond the 100,000 years, then

24:16

there are just a handful of studies that have

24:18

been done on such old samples. And

24:20

so that is the time period that we

24:23

in the paper define as being

24:25

deep time paleogenomics that is beyond

24:27

the 100,000 years. Why

24:29

is it that most studies have focused

24:31

on such recent ancient DNA as

24:33

opposed to the older Pleistocene DNA?

24:36

I think there are a couple of different houses

24:38

to that. One is that a lot of people are focused

24:40

on humans and there's a lot of interest in

24:42

their sort of archeological community about

24:45

how human society is developed.

24:48

And for that, there's been so much changes

24:50

happening in the last 10,000 years that makes

24:53

it interesting. For that reason, because of the

24:55

focus on human samples, I think is one explanation

24:57

why most of the work has been done on

25:00

more recent times. But perhaps

25:02

an equally important one is radiocarbon

25:05

dating. Radiocarbon dating is

25:07

extremely powerful in estimating

25:09

the age of bones and teeth, but it only

25:11

works up to about 50,000 years. So

25:14

any sample that is older than that, then

25:16

you can't get an accurate radiocarbon date

25:18

for it. And that of course makes it a

25:20

bit more complicated in terms

25:22

of just sample availability, because

25:25

if you want to work on samples that are

25:27

say 200,000 years old, then you also need to know

25:29

that they are indeed that old.

25:32

And radiocarbon dating is kind of

25:34

the best way to do that. And that only goes back a

25:36

certain amount of time. Yeah, and then

25:38

of course the third explanation is that the older

25:40

sample is in general,

25:42

the more difficult it is to get DNA from it. So

25:44

if you're moving back into half a million

25:47

or a million years ago, you're not exactly picking

25:49

the low hanging fruit of ancient DNA, or

25:51

much of the sort

25:53

of environmental changes that

25:56

are really interesting. If you're trying to understand

25:58

the processes that... kind of create

26:00

a biodiversity we see today. They

26:02

happened on the time span between 100,000 years

26:04

ago and say 2.5 million years ago.

26:08

Right. What kind of has changed in the technology

26:11

and in the ability of scientists

26:13

to gather that data that has allowed

26:14

for these older fragments of DNA

26:17

to be processed more quickly and

26:19

better? There are a couple of different breakthroughs

26:22

or developments that have helped this,

26:24

I think. That's the most important one

26:26

is the revolution in DNA sequencing

26:29

technology that has kept going

26:32

over the last, say, 15 years. Because

26:35

many of these really old samples, they have extremely

26:38

little endogenous DNA. Some

26:40

of our really old mammoths, for example, they

26:42

have only one or one and a half, two percent

26:44

mammoth DNA. The rest is DNA from

26:47

the environment and from bacteria. And

26:49

if you go back to the years 2008, 2009,

26:51

2010, it would seem to have been too expensive

26:56

to do a project on this. But

26:59

now, DNA sequencing is so cheap that

27:02

it is actually possible even when the samples

27:04

are really bad. So that's, I think, the primary

27:06

reason. But there have also been a number

27:09

of technological developments on

27:12

the actual DNA extraction and

27:14

library construction front. There

27:16

have been improvements in DNA extraction

27:19

methods that have been focused on really

27:21

pulling out the very short fragments from

27:24

the DNA extracts. So today's methods

27:26

are better at this.

27:27

So what are kind of the processes that have shaped

27:29

biodiversity and why has that sort of happened

27:32

in this

27:32

deep time period rather than more recently?

27:35

I think that the main process that has shaped

27:37

biodiversity throughout much of

27:39

the world, at least in high latitude

27:42

and temperate regions, are

27:44

the glacial cycles. And so

27:47

Earth entered into a period of ice

27:49

ages starting already two

27:51

and a half million years ago. And then there's

27:53

been a long series of ice ages.

27:57

These have shaped a lot of the biodiversity we see

27:59

today. And in order

28:01

to study that, it might actually be of interest to

28:03

not only study the end of the last ice age,

28:06

which happened about 10,000 years ago, but

28:08

actually to study multiple glaciations.

28:11

And there are a couple of features that are, I think,

28:13

of particular interest. So

28:16

for example, you have an extremely

28:18

long interglacial about 400,000 years ago called MIS-11.

28:22

I think it would be very interesting to try to understand how

28:24

that interglacial that lasted four

28:27

times longer than most other interglacials, how

28:29

that affected biodiversity, especially narptic species.

28:32

But there's also a transition roughly

28:34

one million years ago where the ice ages become

28:36

longer. So before that, ice

28:39

ages are about 40,000 years old, but after

28:41

a million years and going forward almost

28:43

present day, the ice ages were typically 100,000

28:46

years old. Interesting.

28:48

And so these glacial periods, is

28:50

it mostly a temperature thing that's causing

28:53

these sort of changes in diversity

28:55

particularly?

28:55

I think it's primarily the temperature. And

28:57

of course, one needs to remember that cold-adapted

29:00

arctic species, for example, they will have been

29:02

expanding their ranges during glaciations.

29:05

They had a much larger range during the last

29:08

ice age and presumably during previous ice

29:10

ages. Whereas temperate species,

29:12

such as red foxes or red deer, they

29:15

will have contracted into refugia

29:17

during ice ages and only expanded

29:19

during these much shorter 10,000-year-long warm

29:23

periods. So there is this kind of dance,

29:25

if you wish, between the arctic and the temperate

29:27

species where one is expanding, the

29:30

other one is contracting and vice versa.

29:32

Got it. And that's something that we're kind of seeing today

29:34

as well. You're talking about a little bit the arctic foxes

29:36

and the red foxes. Absolutely. I

29:38

did my PhD on arctic foxes in a picture. I'm

29:41

quite familiar with those. But yeah, I mean, today

29:43

what we see is that their range is contracting

29:45

because the red foxes are expanding

29:47

their range and red foxes will out-compete

29:49

arctic foxes. They are about twice as large.

29:52

So you're talking a little bit about this potential

29:55

for ancient DNA to help with understanding

29:57

this biodiversity shift that's happening.

30:00

happening over these glacial periods. Why

30:02

are paleo genomes so integral to understanding

30:05

that and what is what you're hoping that you'll be

30:07

able to do with this new ability to

30:09

look

30:09

at these ancient genes? Paleo

30:11

genomes are a bit like using a time machine

30:14

that gives you the opportunity to actually

30:16

go back in time and sample DNA

30:18

at different points in time so you

30:20

can create this kind of genomic transects that

30:23

span interesting time periods. That

30:26

is in many ways a much more powerful

30:28

way to study evolution than only

30:30

relying on modern genomic data

30:32

because then you have to use inference to

30:35

try to model what happened in the past. With

30:37

ancient DNA you can go back and you can measure exactly

30:40

what happened. With modern DNA and inference

30:42

you can't see if there was a whole plate

30:44

or a whole lineage that went extinct.

30:47

Interesting. So it's kind of resurrecting the

30:49

images that we wouldn't have known about otherwise

30:51

through the models that we have. Exactly.

30:53

And I think some of the things that have come out of this

30:56

recently, I know you mentioned the paper there was

30:58

a study about brownberries and how

31:00

they are

31:01

hybrids or that this mesh of

31:03

these other species.

31:04

What are kind of the most

31:05

fascinating things that you see have the

31:08

potential to be worked on with space?

31:10

I think one of the main things that we are seeing

31:12

in ancient DNA in general, but perhaps

31:15

even more so when we go even further

31:17

back in time, is how important hybridization

31:20

has been for the evolutionary process. I

31:23

was familiar with the fact that most humans,

31:26

at least humans outside Africa, carry a small

31:28

percentage of Neanderthal DNA and

31:30

many populations also carry the Nissivan DNA.

31:33

But we now also know for example that brownberries

31:35

carry DNA both from polar bears,

31:37

from an ancient hybridization and from cave

31:40

bears. So about between two

31:42

and four percent of the brown bears DNA

31:44

is actually cave bear DNA. And

31:47

in a study we did and published a

31:49

couple of years ago on mammoths, we could

31:52

also show that the

31:54

North American Columbian mammoth is actually

31:56

a hybrid between on the one hand

31:58

woolly mammoths and on the other. On the other hand, that previously

32:01

unknown type of mammoth that we

32:03

call Castocca.

32:04

It makes it then a lot more complicated than just

32:06

these

32:07

branches of the cladogram where you've

32:09

got all these different species sort of

32:12

separate. They all will end up mixing. It's

32:14

increasingly so that instead of

32:16

this classical view of evolution

32:18

where everything is branching into a sort

32:20

of a tree-like structure, it looks

32:23

more and more like we have a weave of

32:25

different lineages that disappear,

32:28

that coalesce together,

32:30

that merge, where there's gene

32:32

flow between lineages and so on. So I

32:34

think evolution and life is turning

32:36

out to be a bit more complicated perhaps

32:39

than the traditional view. Exactly. Yeah.

32:41

You also mentioned in the paper that there are still

32:43

some challenges to bringing this nice gene

32:45

DNA to the mainstream. What

32:47

ideas are you and other scientists

32:49

working on to make these paleogenomes more

32:51

useful and more accessible and enabling

32:54

more science to happen with this data?

32:56

Well,

32:56

we think that there's still quite a lot of scope

32:58

to improve the lab methods, both

33:01

in DNA extraction methods that are more efficient

33:03

and as well the library construction

33:05

methods. There are previous studies that

33:08

show that you lose quite a large

33:10

percentage of the DNA during this process.

33:14

That's one area where there is definitely scope

33:16

for improvement. The second area I think is

33:18

also in the bioinformatics. Also

33:20

in the actual data analysis, because as

33:23

the DNA fragments get shorter and shorter, they're

33:25

also more difficult to map

33:27

to the reference genome and you get lots

33:29

of various biases that could lead to

33:32

erroneous results. So there's definitely

33:34

a lot of work that needs to be done on

33:36

extremely degraded DNA fragments

33:39

and how we deal with those bioinformatically.

33:40

It sounds like you've got some exciting stuff

33:43

ahead. Thank you so much for coming on the podcast,

33:45

Luve. Thank you. I enjoyed

33:47

this.

33:47

This was fun. I'm Luve, and I'm an evolutionary

33:50

geneticist at Stockholm University.

33:52

You can find a link to the review we discussed at

33:54

science.org slash podcast.

33:56

And that concludes this

33:59

edition of the Science

33:59

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34:32

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34:33

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34:34

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