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August 28, 2024 18 mins

Professor Turi King, director of the Milner Centre for Evolution, discusses Dr Nick Priest's research paper into the identification of the multiple drivers of cactus diversification, published in Nature Communications.

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(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 Nick Priest, who is lecturer in evolutionary biology, about his new research identifying the
multiple drivers of cactus diversification, which is out in Nature Communications.

(00:25):
Now, Nick, before we talk about this new research, I know you had a really interesting paper which
came out last year that was looking at the diversity in orchids. And I know Darwin also
studied orchids, and he proposed that orchids had evolved over a really long time, with species
adapting to attract different pollinators. But what you and your team found showed that that

(00:47):
wasn't actually the case. So, talk me through, what were you looking at and what did you find?
In the middle of the Covid pandemic we had a huge shift in what the lab did because we
couldn't do our research. So, we came up with this project looking at diversification of
this group of plants that Darwin had worked on.And what my PhD student, Jamie Thompson,
found was that when you look at the phylogeny of a group of orchids,

(01:10):
the terrestrial orchids, which it turns out was the group that Darwin was so fascinated with,
there's a very conspicuous pattern, in that most of the species appear to arise fairly recently.
And when you look across the history of the planet Earth, the pattern of the relationship
between different species, it's very conspicuous in the orchids. Why did so

(01:32):
many arise so quickly? And it turned out this was the big dilemma that Darwin was facing all those
years ago. And it was sitting there right in front of us in the terrestrial orchids.
So basically, what you've got, kind of like a family tree essentially of terrestrial orchids,
and you're looking at like, when are these branches arising? And you were finding that a lot

(01:54):
of them arise all at once. Why is that happening?Yeah. So, once you have a phylogeny,
then it turns out with modern statistical methods, there are ways of testing what are
the possible causes to explain that pattern.And of course, the big one we had to exclude
was the one Darwin thought, that they must be around for eons,

(02:15):
and so it must have been inconsistent with just a gradual evolution of different species.
And by testing different hypotheses, for example, changes in carbon dioxide in the Earth's history,
or even the well-known changes in sea level that happened, we could then exclude a number
of hypotheses, and through other kinds of tests, we could work out that it really

(02:37):
had to be temperature change in the Earth's history that drove it, not other types of
climate change or time, or even pollinators driving the patterns across the whole group.
So how do you work out when this kind of sudden change happened? How do you work that out?
Yeah, I got to admit, this is one of the dark arts of evolutionary genomics. For a long time,

(02:59):
we've known about techniques in molecular clocks that allow us to time when various events happen.
What makes it particularly difficult in this group of plants, as it's true in all succulent plants or
plants, that don't leave a residue in the fossil record, is that we don't have rocks that we can
use that we know happened at a particular time to, sort of, cement when it happened.

(03:22):
In this case, we relied heavily on changes in plastid genomes to give us inferences.
And this was considered a gold standard for explaining changes in orchids and
other related plant groups. So, by working very, very carefully with established timing points, we
then had confidence of when these species arose, and that allowed us to then test which potential

(03:48):
ecological hypotheses could be driving it.So essentially what you can do is you can
look at the DNA of various species. We know that there's genetic differences between them,
and we know that those differences, those mutations that cause those genetic differences,
they happen on kind of a regular, sort of, basis, so you can use them like a clock. So, this is that

(04:11):
molecular clock that you're talking about.So, by looking at those differences you can
start to time as to when all that coalesces back to. And you found that this radiation happened
about 10 million years ago, is that right?The origins of the orchids date back much
longer than that. But when we look at when did the big burst happen, the new species happen,

(04:31):
it all happened really in the last 10 million years, which may seem like a long time to
your listeners here, but actually, in the eye of evolution, it's a blink.
And it's when climate change was changing, but not how we think now,
where we know everything is getting warmer. This was when stuff was getting cooler, wasn't it?
Yeah. This is the major ice age that people talk about, where the major glaciers formed,

(04:53):
and we can still see residues of the glaciers. In fact, a lot of the most depressing news
stories we see are those glaciers falling apart, that came about during that era,
where the global temperature precipitously dropped for a whole number of reasons, and for plants in
particular habitats who can't move, there then trapped in environments that aren't as suitable

(05:15):
for life. And we think it was that probably with other patterns that we haven't yet explored,
haven't yet explained, that then drove it. But it was certainly triggered by this cooling event.
And do we know why cooling temperatures did this or is that your next question. We can
see that that's what's happening, but we don't know quite why it's happening. Or
do you know why it's happening?No, we have absolutely no clue.

(05:39):
I want to give a shout out to my cousin Gretel Kiefer, who turns out is one of the
world experts in a single type of orchid.She has a 30-year data set of the western
fringe prairie orchid, and she's shown that this orchid, its seed set changes
from year to year. And there might be related to changes in climate that she's observing.

(06:00):
Now, if she can observe that in one species that you see major variation happening in
reproductive output, it's not too surprising that this could be simultaneously happening
in many, many species at the same time.This is what you were finding in orchids,
and then you, kind of, turned your attention to cacti, which I didn't realize is one of the most

(06:20):
endangered of any taxonomic lineages. So, tell us about cacti. So, what's the starting point
for your research when you're starting to look at cacti, you're one to know about what's driving
diversity. What was the thinking at the time?Yeah, I got to say, most of this is because we
thought cacti are cool, and as a group, it fit the same thing as the orchids in that

(06:41):
it has a huge number of species, and they seem odd. But once we had information that
orchids could be driven by climate change, it made us think, well, what about other groups?
And if we dug down deeper, could we find specific aspects of climate that
are driving diversification of other groups, and the cacti just seem like a great group.
One thing I want to add to that is there have been lots of hypotheses about what

(07:05):
could be driving diversification in cacti. From my quick look through, I found at least
25 different hypotheses out there, that actually seemed reasonably well supported.
But of course, it doesn't make sense that so many things could be driving diversification. And so,
we had to think carefully about the approaches we used to then test patterns in cacti,

(07:26):
and not just be another one throwing up another hypothesis but trying to do it more concretely.
So, what did you do?Yeah. So, we turned to the power
of artificial intelligence. And there's some features about AI that make it really good for
testing lots of hypotheses simultaneously. It just has an efficient configuration.
So major problem in evolutionary biology is we just don't have the computer power to

(07:50):
understand shifts across entire phylogenies, with thousands and thousands of species,
across thousands and thousands of traits, in thousands of thousands of locations.
It's just a computational problem. But machine learning is set up to make that very efficient.
And then the other neat feature of machine learning is, it allows you to specify the

(08:12):
level of complexity that you test with the data set. So, we could address a whole set of different
hypotheses simultaneously and test for what are the effects of each of them individually. But
then we could also just change the dial to allow us to then test for how do these factors interact,
and could it be multiple forces driving? And if you consider multiple forces working together

(08:35):
driving diversification, then it might actually be a different list that we would identify as
being important for diversification.So, what are the various things you're
kind of trying to feed into this to find out which has the most influence?
Yeah. Well, this I got to give a lot of props to my PhD student, Jamie Thompson, about this,
because he quickly realized that there were a set of different data sets that we could apply.

(08:57):
And so in addition to having the phylogeny, we then worked out what are the climatic variables
all across the Earth and then bringing in other information about soil quality,
geographic factors, on top of things like chromosome number counts, we can then
assess a whole set of questions independently, once we had built this big data set, then we

(09:18):
could explore how those factors contribute to the evolutionary patterns we can see in the phylogeny.
So that's really cool. So, you can feed in all of this information basically into a computer
program that then goes, right well, it's working out how these things are interacting and what
seems to be the most important factors in driving speciation and diversity. And what did you find?

(09:40):
Yeah. So, after all that, testing 39 independent hypotheses across the entire phylogeny,
the three that came up were not what the experts would have predicted as being essential drivers.
We would have thought that it was pollination driving everything. And in fact, that was one
of the major features that Darwin focused on, and it made complete sense and still
makes complete sense, and it still may rue the day once we get better data, but it didn't pop

(10:05):
up as being a central driver in our analysis.So, it turned out that diurnal temperature range,
so just what the plant experiences in its location on a day-to-day flexibility.
When we think about cacti, they look they look, kind of, a prototype example of a succulent plant,
which has a fleshy surface that we know is really good at capturing water and maintaining water.

(10:29):
And so, we would have thought that it was due to the dryness in the air, the aridity,
that must have caused it, because it seems like, oh, well, they're so good at capturing
water. And so, we thought, well, they must be diversifying where it's driest,
but actually they're in wet climates as well. And there's a huge variety of forms, and so we
quickly turned to cactus experts for our help.And we were so fortunate to have Tanya Hernandez

(10:54):
join in on the team, and she was a huge asset to giving us an understanding of
the ecology, and also why we might not expect aridity to be such an important driver.
So, what are the other ones besides this temperature thing?
So, the one that surprised us the most was the second highest rated variable,
which was the sand content of the soil, and then the size of the plant came out.

(11:20):
Now, the one thing about these machine learning analysis is when it pops up, as something like,
oh, here's the variable that's important. It doesn't actually tell you what the pattern is.
And when we did some intense mapping onto it, it turns out it's very small cacti and very large
cacti that diversify rapidly, and they maybe diversifying for different reasons. But it was

(11:40):
those two extremes that worked out, for example.And then just to add in that the isothermality,
the daily variation in temperature, and then compare that to annual variation in temperature,
it measures the ratio of the two. How important is an annual variation relative to a daily
variation. And I think one thing that gives us some confidence in this is that it turned out

(12:04):
it was an intermediate isothermality, which means that the daily fluctuations are about
half of the variation in the annual fluctuation. So that seems about right in terms of it's not
saying it's super extreme, and it happens enough across the cactus phylogeny that
we're pretty confident that that's important.And the only other last variable was geographic
size. It's a funny variable because it basically looks at how the coverage of species across

(12:29):
vast terrain. So, in some ways, a large geographic range kind of makes sense,
that maybe there's more opportunities to find special niches where then it can diversify. So,
it turned out that the geographic range also explained patterns of diversification.
So why do we care about what's driving evolution? So, evolution is essentially where you get

(12:50):
diversity. So, diversity starts at the genetic level and then it's selected for. So, there might
be things that are making it more advantageous or disadvantageous in particular regions or areas
or whatever. Why are we bothered about that?Well, I think anyone that looks at the changes
that are happening in our climate now, does make you wonder what's going to happen. And

(13:14):
what basic evolutionary biology tells us is if there's genetic variation and there's variation
in responses to selection, then are going to get an evolutionary response. We're going to
see a conspicuous change in the nature of the species we're looking at. That's something
that micro evolutionary research has told us.What we're trying to do with this kind of research

(13:38):
is essentially map on the micro evolutionary insights into the macro evolutionary patterns.
So, if we can identify the ecological drivers for macro evolutionary patterns,
it can give us insights into those smaller changes happening within populations of organisms that are
driving populations in particular directions, that could then change organisms across time.

(14:03):
So, I think we care because it's how we got here, and we care because it's where we're
going. And I think this type of approach that mixes insights from macro and the micro is,
sort of, at the frontier that hasn't been explored much, and frankly couldn't be explored until we
had broad data sets available to us and then the computing power to be able to test for it.

(14:29):
And you found that temperature is one of the main drivers, and that's obviously really important,
as you've already alluded to, to some extent, with climate change.
Yeah. So, you might say, well, what we learned with the orchids isn't relevant here because
that's a global cooling, not a global warming, right. But it could well be that it's really about
the temperature extremes, or it could well be that extreme cold period then created an environment

(14:54):
that wasn't hospitable for the pollinators, which then caused problems for the plants.
I should say that although we've excluded pollinators as being the drivers, that's
just what the evidence we have tells us. With better data, we might have a
more informed picture. And I should point this out that in the case of the orchids,
we were able to show that diversification is 700 times more likely to be driven by global cooling,

(15:17):
than just the time that Darwin had envisioned.But we still haven't explained all of
biodiversity, and in the case of the cacti, it's more than 70% of the variation is unexplained,
which means we either need better data sets or better methods in order to work out what's
actually been the major factor driving it. We're chuffed to bits that we were

(15:37):
able to identify important drivers, but there's still a long way to go.
So, Nick, what's next for you?We've established now that there is
this effect of global cooling on orchids, and there's climatic effects on cacti,
we're also investigating general effects across all succulent plants, trying to work out

(15:59):
the timing of the evolution of succulents. But it still gets back to this general question of,
now that we've learned so much about climate, can we apply it to tell us something about
whether we are at a tipping point in evolution?And Jamie and I've had a thought of putting
together a collaboration of scientists to get at, whether these tipping points are happening

(16:19):
across lots of different groups of plants. One of the ones I'm most interested in is the ferns.
So, working with ancient groups of plants and studying their patterns of diversification
might give us more information. So, what might be possible, if climate has had such a
big effect in evolution, if it does contribute to these tipping points, then we should see a

(16:41):
residue of that in the fern phylogeny as well.And what we'd like to do is build models that
allow us to identify not just global cooling events, but global warming events as well,
and then identify the temperatures at which those bursts in speciation and extinction happen.
So if we had a catalogue of hundreds of plant species, and when their big diversification

(17:06):
events happened and how that relates to climate change, then it might give us a
lot more confidence about whether the global warming we're now experiencing is a serious
problem or actually we still have another five degrees to go until the species start crumbling.
I think this type of research is something that there's a lot more active engagement in,
but I do think our study contributed to showing the clearest pattern of

(17:29):
temperature driven diversification to date, and I'm hopeful that we can build the team together
to then assess this across all plant groups.Nick, thank you so much for talking with me.
This was a podcast by the Milner Centre for Evolution at the University of Bath.
I'm Turi King and thank you for listening. If you have any thoughts or comments on this

(17:52):
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.
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