Using Genomics to Understand the Evolution of Plants - Dr James Clark

The Director of the Milner Centre for Evolution, Professor Turi King, talks to Dr James Clark about his research into plant evolution.

Episode Transcript

(00:02):
Hello and welcome. You are listening to a podcast by the Milner Centre for Evolution,
at the University of Bath. I'm Professor Turi King, your host, and today I'm talking
to James Clark, who is a prize fellow in theoretical and empirical evolution,
about his research into plant evolution.James, I know incredibly little about plant

(00:28):
evolution. So, in brief terms, talk me through what do we know about how plants evolved?
Where do we think they came from?So, plant evolution in a nutshell,
is all about the movement from water to land. Plants as we think of them today originated
about half a billion years ago, and they would have come from something that would have looked

(00:50):
a bit like algae do today. And it was this movement from water to land that kind of
forms this narrative. And it's how we define a plant, is its ability to survive on land.
So, whereas they were living in water before, which is obviously a very wet environment,
the main challenge for plants has always been, how can I survive an increasingly dry and inhospitable

(01:17):
environment? So that is kind of yeah, the origin of plants, kind of in a nutshell.
So, when is this thing happening where plants are coming up onto land?
See that's something that I'm really interested in, and it's actually a really
big unknown. We think that plants came up about half a billion years ago, but we can't be 100%

(01:39):
certain. And the reason for that is that by the time we get fossils of things which are
recognizably plants, they're 100% plant.So those transitional forms that we’d be
looking for, you know, something that's a little bit algae but a little bit plant,
we don't have any of those. Instead, by about 420, 430 million years ago, we have got plants

(02:03):
with rooting structures, stomata, which are tiny breathing pores which allow gases in and out,
they're producing spores. We can see axis, so kind of the vertical structures that we
associate with plants. So that's all there.So, the big mystery and something I'm really
interested in is, well how did we get from algae, that look like pond scum, to more or less

(02:26):
a complete plant without a fossil record.So, what are these first plants looking
like in the fossil record?Well, that's also one of the
biggest disappointments of the field, is they look rubbish. They are lacking what you could
call the most charismatic features of plants. So, there were no flowers, there were no leaves.

(02:47):
None of the kind of beautiful, elaborate structures that we really value in plants.
They were more or less single axis. So just a single green shoot that probably
grew as a mat. So, with structures we call rhizomes, which are what they used as roots,
but they're more or less just horizontal shoots that would have covered the ground.
They would have grown a few millimetres tall. So maybe the closest analogue in terms of visual

(03:13):
identity would be mosses or other non-vascular plants that we find in very damp areas now.
So, you're almost looking for kind of like the missing link between algae in the water and these
early plants. You're trying to understand what's gone on in between there. How do you do that?
Yeah, it's a really interesting challenge. So, we've got a big gap in the fossil

(03:38):
record. And that for a period had left us pretty much stumped. But what we're
looking at now is evidence from within the genome.So, if our genome could be considered a blueprint
for how to make a plant, then we can look at all of the different living plants that we have
available, mosses, liverworts, ferns, flowers and we can compare their genomes, and we can then try

(04:06):
and trace well, what's the same? What's different? And we can do that in more sophisticated ways with
evolution models, until we can arrive back at what we think the earliest genome was like.
So, this gives us an evolutionary blueprint that could take us all the way back to the first plant.
And from that we can then try and say, well, okay, we're seeing this gene and we're seeing that gene.

(04:29):
Maybe it had one copy of this gene or ten of this. And from that we can say, okay, well, these are
genes to do with roots. And if all of the genes that might help us produce a root are present,
then maybe the first plant produced roots.So, you must be looking at genomes across loads of

(04:50):
different types of plants then to try and do this, this must be computationally quite tricky thing to
do. What are you doing? How are you doing this?Yeah. So, the more genomes we have available to
us, and from the greater diversity of plants and those algae that are closely related, the better.
And what it involves really is to try and find the common genes in all of these different plants.

(05:17):
So, if we have a gene that we think controls the response to UV, ultraviolet light,
one of those key stresses in plants. And we know from experimental evidence that this gene turns
on the response to UV. We look for that gene in all of the living plants. And what we tend to see
is a mosaic of genes across different plants.We find that it's missing in certain plants.

(05:43):
We find that the gene has duplicated, so multiple copies of a gene can form families within certain
plants. And sometimes this is very intuitive. So, if we have a plant which grows in the understory
of a rainforest, as a lot of ferns do, then we find that that gene's been lost,

(06:06):
it no longer needs to respond to UV, and so that's gone. And likewise, plants growing in
the desert might have produced more of these genes to try and fine tune the UV response.
So, you see these environmental responses at the level of genes and it's by tracing the presence,
absence, the number of genes backwards in time that we can try and make these inferences.

(06:29):
And presumably, as you say, you're looking for genes that seem to be basic for being a plant. So
are you kind of looking at all of these kind of conserved genes that are across various plants,
but also taking into account, well, we think the environment would have been this. So,
we think it's almost certain that the early plants would have had that in their genome.

(06:52):
Yeah. It's a really interesting problem because we're not 100% sure what that environment was
like, we have some insights into it. For example, there's a very famous fossil locality in Scotland,
it's called the Rhynie chert. And this is perhaps the best-preserved fossil site
we have for early plants. We can get 3D axis of these plants. We can see them all the way

(07:17):
down to the level of individual cells.We also know that this environment was
probably similar to how Yellowstone is now, so it was a hot spring environment.
So, we've got this wealth of information about early plants. We don't know how typical these
plants were of the time, or whether these were already adapted to a quite unusual
environment. And it's the same with the genes.So, we can predict what genes do in living

(07:42):
plants. But maybe they were doing something different a long time ago. And the best way
we can get around this is to compare gene function in as many plants as possible.
So, we tend to work with flowering plants, they're our most lab ready specimen. And
increasingly in the last decade or so we've been looking at a greater diversity of plants.

(08:05):
So, things like mosses and liverworts, we're now able to grow in the lab. We're able to do the
same genetic experiments to try and determine gene function. And if we find the same gene function,
say, in a moss and in our flowering plant, then that's a really good evidence that the gene was
probably doing the same thing in the first plant.If it's doing something different, then that's

(08:28):
another problem. And really, it's a big headache, you know, how can we infer the ancestral
function of a gene when it's doing something completely different in all of its descendants.
So why do you want to know this? What can you use this for? If you know what the first plants
look like, what can you use that information for?So, on one level, I just think it's fascinating.

(08:53):
It's the origin of the terrestrial environment. Like I say, without plants there wouldn't have
been animals on land. So, it's really a singular event in the Earth's history
that kickstarted everything. And I think that's fascinating, and I desperately want
to know what was going on at that time.The other thing is that we're looking at

(09:14):
the origin of plant traits. So, these are the features of plants that have evolved over time.
And we see them in a lot of crop species.So, for example the leaf, you know,
leaves are very important. They control the rate of photosynthesis and the environments
that a plant can survive in. And so, if we want to understand how a leaf forms, you know, we can

(09:36):
zero in on our favourite crop species. Or we can take a broader view and we can ask, well, this
plant has very broad leaves, it photosynthesize is very efficiently, this plant has no leaves
at all. So how do we get from one to the other?So, it's using evolution to try and understand
the origin and diversity of traits that are really important to crops.

(09:59):
So, you're essentially looking at the entire genome of various plants. So
how are you using genomics in your research?So, I'm really interested in how the genome
has evolved, at almost the level of the entire genome. And that's
another reason why plants are so amazing.So, plants have the largest and also the most

(10:24):
variable genomes of all living things. So very recently it was shown that the largest genome
of any living being belongs to a tiny fern that grows on a Pacific island, which is amazing. They
also have more chromosomes than any other living thing, so some of them have over 1400 chromosomes.
So, there these bizarre genomes and all of this strange, wonderful evolution is telling

(10:51):
us a story. And that is how from this first plant, that we don't see in the fossil record,
has subsequently evolved to produce the hundreds of thousands of plants that we see today. And so,
we're using genomics to try and understand what has allowed all of this diversity to evolve.

(11:12):
So, we know that there's kind of waves of extinction, so the biggest one that
everyone knows about is dinosaurs. But do you get the same thing happening in plants?
Yeah. So, the big extinction events affected plants as well. And there are whole groups
of plants that once existed that are no longer alive. And chief among these, and some of the most

(11:33):
interesting, are a group called the seed ferns.So, this is where the seed as a reproductive organ
evolved, and they grew somewhere between a living conifer and a living fern. So,
these were tall, upright, woody trees that sent out curling fronds, like living ferns
have. But borne on the end of the fronds were seed producing structures, so these were a real

(11:57):
intermediate between ferns and the seed plants.And do we know why they went extinct? What
was it about them that made them go, nope, can't deal with this?
We actually think that they were ultimately out competed by the living groups of plants,
so things like conifers. And we do see successions of different floras,

(12:18):
so early vascular plants were replaced by ferns. And subsequently these seed ferns evolved but were
then replaced by conifer like plants.And then kind of the most recent innovation
of plants is the flower. And we're really living in the era of the flower. So flowering plants

(12:39):
make up 90% of plant diversity. And so, we're in their heyday and they are expanding where
all of the other plant groups contract.So, James, you can tell you find this
really fascinating. So, what has been, kind of, your biggest discovery so far?
So, when we looked at the genomes of all of these living plants, we were actually able

(13:01):
to reorganize the family tree of all plants. And what we found has really big implications
for our understanding of the earliest plants.We had thought, as recently as five years ago,
that plants evolved along a progression. They became larger, more complex, we saw things like

(13:25):
vasculature and leaves progressively appearing.But now that we've got this new understanding
of how they're related to one another, we don't actually know what the first plant looked like.
It's throwing up a huge question mark as to what the nature of the earliest plant was.
So instead of it being kind of this gradual progress forward,

(13:47):
from these kind of more simple plants, without the vascular system, to kind of vascular plants,
you've actually found that they kind of split in two relatively early on, and then evolved.
Yeah. So, it's a fundamental split in the plant lineage. We now know that there are
actually two distinct groups of living land plants. So, the vascular plants and

(14:07):
the non-vascular plants. And we didn't know how these were related to each other before, but we
now know that they are evolutionarily distinct.And what we now don't know is, was the earliest
plant more similar to the non-vascular plants. So did it lack vasculature and all of the
advantages that come with it. Or was it like a vascular plant, could it already move water

(14:29):
around in a way that's actually much more advanced than we might have first thought? And this is why
we're now drilling into the genomes to try and help us answer some of these questions.
So, James, what's next for you in terms of what you want to look at?
So now we have all of these new genomes, and we have a much better idea of plant evolution. So,

(14:52):
what I want to do is to start to understand the genetic and the genomic evolution of plant traits,
and to understand how that relates to the diversity of crops that we see today.
So, we could take a trait such as stomata, the breathing pores, which is so important for plants.
And if we can understand their evolution and the diversity of stomata across plants, we might be

(15:17):
able to better engineer stomata in crop plants to improve water use efficiency and help them
to survive in increasingly dry climates.So, this is linked into climate change,
sounds like?Yeah, absolutely. So,
plants are key engineers of our climate, but they're also responding to it. So, it's likely
that as the climate changes we're going to see differences in plants ability to respond, and in

(15:44):
particular crops, which are not particularly well suited to surviving on their own.
So, it's really important that we understand the traits that allow plants to survive in warmer,
drier, wetter, more extreme conditions.James, thank you so much for talking with me.
This was a podcast by the Milner Centre for Evolution at the University of Bath.

(16:07):
I'm Turi King and thank you for listening. If you have any thoughts or comments on this
or any other episodes, please contact us via our X channel @MilnerCentre.
For more information about the Milner Centre for Evolution, you can visit our website.