The Revolution in Plant Evolution

Good evening, everyone. It’s a tremendous pleasure
to introduce Pam Soltis. Pam is Distinguished
Professor and Curator of the Florida Museum
of Natural History at the University of Florida. And Pam is, by all accounts,
a brilliant scholar and leader in the field of plant
evolutionary biology. So Pam, it’s a real treat that
you could be here tonight. Thank you. Thank you. So Pam currently leads
the renowned Laboratory of Molecular Systematics
and Evolutionary Genetics at the
University of Florida, where scientists collaborate
on a variety of questions investigating
mechanisms of plant speciation and
evolutionary relationships, especially among
flowering plants. And I think it’s actually
worth taking sort of a step back, though, and really
recognizing and acknowledging the sheer breadth, both in terms
of the organisms of interest and the questions in
which her lab is focused. So they really span
all of land plants. So here we’re talking about
huge groups of species across deep evolutionary times. But they also focus on very
recent patterns of speciation. It’s quite dynamic. Pam received her
B.A. in biology summa cum laude at Central
College in Iowa. And she went on to complete
both of her advanced degrees, master’s and Ph.D., at
the University of Kansas, which is a real hub of
organismal research. And again, her research includes
investigations of the evolution of flowering plants. She’s also interested in
the conservation of genetics of rare plants as well as
historical processes that govern the geographic
distribution of plants. She’s really
considered a pioneer in her work
understanding the origin and evolutionary significance of
chromosome evolution in plants. And she’s been at the forefront
of really aggregating as well as producing enormous amounts
of especially molecular data and synthesizing
them in novel ways to understand plant evolution. She’s received a ton of awards,
too many really to go through. But I did highlight four here
that were worth mentioning. The first is
effectively the sort of botany equivalent
of the Nobel Prize, and that is the 2002 Dahlgren
International Prize in Botany from the Royal Physiographic
Society of Lund, Sweden. She’s also received
in 2006 the Asa Gray award from the American
Society of Plant Taxonomists, the Botanical Society of
America merit award in 2010, and in 2004 Thomson
Reuters gave her the title of world’s most
influential scientific mind. Astonishing, really. Not surprisingly, she’s
published hundreds– I didn’t actually run
the citation index, but articles in top-tier
journals like the American Journal of Botany, Systematic
Biology, Science, Proceedings of the National
Academy of Sciences, and Nature, as well as
co-authoring several books, most recently a textbook on the
ordering of plant biodiversity. She’s also co-edited books
on the developmental genetics of the flower,
polyploidian genome evolution, and molecular
systematics of plants. One and Two, I think. I actually remember as a
student, not far over there, reading those texts. But she’s also garnered an
astonishing number of awards, primarily from the National
Science Foundation as well as the Mellon Foundation,
totaling millions of dollars. I benefited from one of
those collaborative projects. It was actually my
only source of funding as a postdoctoral
fellow when I was at the University of Michigan. But I think,
importantly, in addition to being just an amazing
scholar all around, she’s also an incredible
mentor and has demonstrated a real ongoing commitment
to teaching undergraduates, graduate training, and I
think especially the promotion of young women in science. So the list of
accomplishments go on. I won’t continue. And instead, I’ll welcome–
please welcome Professor Pam Soltis. [APPLAUSE] Thank you. Well, thanks a lot, Chuck, for
that wonderful introduction. I guess I will just say that
I have a lot of collaborators. And so anything that seems to
be sort of a large contribution is really because of having
a really active lab and a lot of people who work with me. So I’d like to make sure
that that’s all clear. Well, good evening, everyone. Thanks so much for
coming out on, yes, a chilly evening,
although I understand it’s not quite so chilly to
you as it is to me, perhaps. But I’m getting used to it. I grew up in the Midwest, so
I can handle this, I think. All right, so I’d
like to start out by just talking a little
bit about biodiversity. And biodiversity is the
totality of life on Earth– its physical forms, its genetic
forms, its functional forms. And in all, we currently
have about 1.8 million named species. This includes about half
a million plant species. However, we understand that this
is just the tip of the iceberg. There may be 10 times
as many species, or maybe 100 times
as many species as we’ve currently named. And most of our information
about all of these species actually comes not
directly from nature but from our natural
history collections. And in the US alone, we
have probably over 1,600 natural history collections. And these house potentially
1 to 2 billion specimens. Worldwide, it’s
estimated that there may be 3 to 4 billion specimens
housed in our natural history collections. And these collections
can tell us incredible things about the
past history of life on Earth as we attempt to
incorporate this information into various analyses of
molecular data, chemical data, and so on. Now, for centuries our
natural history collections have primarily been
applied to studies of systematics and taxonomy. That is, these specimens allowed
us to compare species and make inferences about how species
might be related to each other. And in fact, it’s interesting
that most new species descriptions come not
from new collections but from new analyses of
specimens that are housed in natural history collections. There was recently an analysis
of some insect collections across Europe in which four
new species were described, simply from an analysis of the
specimens in those collections. But we now recognize this these
natural history collections can provide us with information
on a host of other sorts of topics ranging from genetics,
even to genomics, to chemistry, to species interactions,
to ecology, phonology, biogeography, and so on. And so these natural
history collections, such as those housed
in this building, can provide us with amazing
new perspectives on evolution and the history of life. In addition, these
specimens can help us as we address the
biodiversity crisis and various societal problems. So for example,
understanding patterns of loss of biodiversity
can best be accomplished when we have the
historical records that these natural history
collections can provide. Just as one example,
invasive species have tremendous ecological
and economic impacts, and it’s estimated that they
cost the US over $120 billion per year. They’re particularly
devastating in areas such as Florida,
where I live, because of our extensive coastlines
and lots of shipping and our combination of temperate
and subtropical climates. However, we have a very
difficult time getting a handle on the factors that are
involved in the spread of invasive species. And if we don’t understand
how they spread, it’s very difficult
to curb the invasions. And so we think that
through the application of historical
records from Herbaria and other natural
history collections, we can start to
get a better handle on how these species might
spread in their introduced habitats. Now, unfortunately though,
most of our natural history collections have specimens
that are essentially locked away from
most scientists, and certainly from the public. However, recent analyses
and recent initiatives have promoted the use of
natural history collections through digitization. So digitization– that is,
putting our natural history collections online–
is actually leading to a lot of new opportunities
to use our natural history collections. Most of the digitization
has involved label data. That is, if this is
our herbarium specimen, such as some of the ones
located over there to your left, most of the specimens
will have a label. And on this label we’ll
have the scientific name, the date, the collector,
the location where that specimen was collected,
associated species, various notes, and so on. And this information has been
transcribed in many cases, and is being made
available online. Now, in addition
to the label data, however, we’re also interested
in capturing not just the data but the images
of the specimens as well. And so a number of different
sorts of mechanisms have been developed for imaging
natural history collections, and just a few of
these are shown here. So we have our herbarium
specimen here on the right. Herbarium specimens are, in
fact, one of the easiest things to digitize because they’re
essentially flat pressed plant specimens. So a simple photograph
often will suffice. But there are various other
types of digitization image captures that are
also taking place, and a few of these other
representatives are shown here. So for example, some 3D
reconstructions here. We have some paleo
collections for many insects. It’s not individual
specimens that are imaged, but in fact whole
drawers of insects may be photographed
and then served online. And so we have a number
of different ways in which people are starting to
capture the information found in our natural
history collections and put them online. Now, thanks to a new program
at the National Science Foundation, more and
more US collections are actually going online. Our university is
now home to iDigBio, which is the
National Coordinating Center for the Digitization
of Biodiversity Collections. And this project is
allowing us to ingest from various collections the
locality information, images, and other data, and
then serve the data to scientists and the public. And then associated with
this is the opportunity to develop new ways in
which these data can be used for scientific
research and for education. And in all cases,
we’re interested in the locality data, the dates,
the images, and in some cases, based on the digitization
project, even the vocalizations, for example,
of birds and of amphibians. Now, the motivating factor
behind this new initiative that NSF has sponsored
is basically research. What new research
questions can be addressed by
digitizing and making this information available? So currently there is a
set of 13 projects designed around a specific
research theme. And these encompass
over 200 institutions that range across the country. And so currently there are
data coming into iDigBio from these 200 institutions
in all 50 states. The topics of some of
these research networks are listed here. I’ve highlighted
the first one here, flowering time and climate
change in New England plants. And this is certainly
one of the projects that Chuck’s group is
involved with here. The Harvard Herbaria
are involved with digitizing information
and then recording the dates at which species have flowered. And then this is being tracked
across centuries, in fact, to identify changes in
flowering time associated with climate change. And then, of course, we
have a few other examples listed here as well where
bryophytes and lichens, for example, are being used as
indicators of climate change across North America. There’s a project monitoring
the spread of invasive species in the Great Lakes region, and
then another project that’s involved with pairing
up specimens of plants, their insect herbivores,
and their parasitoids that parasitize those herbivores. And so this is a
multi-trophic layer analysis which is leading to some really
exciting new developments in how we put specimen
data together to enable new sorts of research. And again, there are 13 of
these projects that are now underway that are
designed to harness the power of the natural
history collections. Now, for the most
part, these projects are based on the label data
that I described before. But more and more
of these projects will be incorporating aspects
of the specimen itself, maybe some aspects
of morphology– that is, the general appearance
and shape of the specimens. Now, all of this information
is being stored in a cloud computing environment. And the scale of
this project has led to the development of
new information technology procedures and
technologies as well. And so our project is
actually a collaboration between biologists and
computer scientists in order to enable
this huge influx and serving of
biodiversity data. Now, in case you might be
interested in finding out more about iDigBio, our homepage is
shown here, along with our URL, idigbio.org. And what you’ll see
here is that we in fact have over 26 million
specimens now assembled within this data structure. This is a 10-year project. We’re into year
four at this point. And the community has
really come together to digitize so much
information, and we’re now making that available. Now, it’s possible from
the iDigBio homepage to go to our specimen portal. And the specimen
portal is the place where one can query our database
to ask if there’s information on a species of interest. So you can see, again, here we
have over 26 million specimen records, over 4 million
media records, most of which are images, but more and
more increasingly are also vocalizations and other
sorts of data, films as well as the static images as well. So let’s say we wanted to
actually search for specimens for a given species. We could go to our search page. And let’s say we’re interested
in searching for red maples. So we could enter in under
the scientific name here, Acer rubrum. At this point, we
don’t have applications that will allow
for common names, but we’re working on developing
a link to some common names so that people who are
interested in looking at something that they might
be familiar with from a local natural area might be
able to look those up by the common name as well. But currently it’s based
on scientific names only. And so we get the return. This will tell us how
many specimens there are in the database. And I can’t read what that
says, but there are hundreds. And we also get a map here,
which, when we blow it up, will show us the distribution
of those specimens. The quality of the
specimens varies. So for example,
we probably really do not have a red
maple growing out here somewhere in the
Atlantic east of Jacksonville. But in fact, the majority
of these specimens are probably more or
less accurately described in terms of their distributions. What you may also notice,
if you know red maples, you’ll know that they’re
an eastern species. There may also be
some red maples that have been planted in
other parts of the continent. Or these may actually
represent the herbaria where these are housed. So a word of warning–
you don’t want to take any of these sorts
of distributional data at face value. There will always be
an element of data cleaning where you
actually evaluate the quality of the data. But what this allows
us to do very easily is access information
from herbaria that are located
across the country. And until very recently,
this sort of enterprise was not possible. So if we select a
given specimen record, we can find out more
information about it. Each specimen record
has the information about that particular specimen. It also tells us
where that specimen is housed, which
herbarium it’s located in, or which museum collection
if it’s not a plant specimen. And it also tells
us whether or not there are any associated media–
for example, photographs. And so you can
then click on that and get an enlarged version, and
then also get more information about the specimen itself. So this is essentially our
capability at the moment. We’re working to
enhance the mapping attributes of the portal. And we’re also in the process
of linking this information with other sorts of data. So far, essentially a specimen
is in the data set more or less in isolation. So that specimen may
be linked in some way to its image, its vocalization
if there is one, perhaps a DNA sample, which is
something that we’re working on. But what we’re really
interested in doing is integrating the
specimen information with various other
sorts of databases that are available on a
national or international scale. And so we’d like to be able
to link these specimens or natural history collections
to other sorts of resources– for example, resources on
phylogeny or evolutionary history. And I’ll talk more about
that in a few minutes. Also linking them to
ecology and to paleontology, to our living
collections, particularly to genomics and
our huge databases that we have in terms
of gene sequences, and then various
other repositories. And so we think actually that
these linkages, which we’re just starting to
explore at this point, between iDigBio and any of these
other sorts of repositories that are listed here will
allow us to investigate some new and exciting research
questions that to this point we’ve not really
been able to explore. So the question is, then, what
can we do with specimen data? In the past, as I
mentioned, specimens have been largely
confined to studies of systematics and taxonomy. But now, as we start
to think more about how locality information, the
dates of collection, and so on, may contribute to new sorts
of evolutionary studies, we can see that there are
really a lot of opportunities for addressing a wide
array of questions. So we can monitor shifts in
biodiversity through time, we can track invasive
species, and so on. And the one that I want to spend
a few minutes talking about is what’s referred to as
ecological niche modeling, particularly in association
with climate change. And here I’ll present a specific
example from our own lab as a way to illustrate this. So we’re interested
in evaluating what might happen to the
vast diversity of plant life in Florida under
models of climate change. There are currently over
4,000 species of plants that occur in Florida. We have this great
combination of warm temperate and subtropical climates
that come together to create unique opportunities
and unique habitats. And this has led to some
amazing diversifications. So what we’re interested
in is taking information from the herbaria in
Florida and elsewhere and using that information
to help us understand what might happen to that diversity
as the climate changes over the next several decades. And this is work that is
being conducted primarily by Charlotte
Germain-Aubrey, who’s a postdoc working with me, and
also with huge contributions from Julie Allen,
who’s a postdoc at the University of Illinois. Now, in this project, we’re
modeling the distribution of these plant species at
the current point in time, and then we want to project
those models of where those species might
occur into the future. So we’re taking
location information from herbarium
specimens and coupling that with environmental
data that we can extract from various databases. Things like temperature,
precipitation, soil types, and so on are particularly
important aspects of environmental data. And then we can use
some specific software to model the range
of each species. Now, there are a number
of sets of software that are available for
doing this sort of work, but we’ve actually found
that for certain reasons, many of these approaches are
really inadequate for what we’re interested in doing. And so we’ve actually had to
develop some new methodologies along the way. And this, of
course, has in a way slowed us down, but
also in a way helped us to devise much
better models, we think, for where these species are best
suited under current conditions and where they might
occur in the future. So we’re developing
these models, and then we project them onto
the future climate conditions as predicted by
climate modelers. So we’ve currently developed
models for about 2,500 species, but I’m only going to report
on some models for about 1,600 of these. We’ve used over half
a million data points that have come from
herbarium records. By the time we do all of that
evaluating of whether or not the records are good
records or bad records, we’ve cut that almost in half. Our actual data going into the
models is more like 300,000 and some specimens
rather than the full set. And then, again, we’re
using environmental features such as temperature,
precipitation, and soil to help develop models. So what does this look like? Well, we see as we model
species and project them into the future that there
will be some ecological winners and some ecological losers. The first example here
is Abildgaardia ovata, the flatspike sedge, which is
a relative of the grass family. And you can see a
picture of it here. It’s currently distributed
primarily in southern Florida. And this heat map shows that
this is the optimal habitat in this area. You’ll also note, I’m
sure, that this is also a highly urbanized area. So despite the fact that that
represents the ideal habitat, the habitat is probably
very limited in terms of what’s really
available to this species. Now, as we project a hotter
and drier Florida for the year 2050, you’ll see that that
heat map is much cooler. And in fact, the amount
of optimal habitat is going to be quite
limited as we move forward. Now, in contrast, we
have the scrub plum here on the bottom panel. This is a relative of
the cultivated plum. And currently it’s distributed
in this area called the Lake Wales Ridge. And we’ll come back to that
area a little bit later, but I do want to point
out that we do actually have a little bit of
topography in Florida. This is a ridge. It gets up to about 300 feet. And when you’re
on top of it, you can actually tell that
you’re on a ridge. And this is an amazing area
because it was actually the only part of
Florida that was not underwater during various
parts of recent glacial cycles. And so there’s a
unique flora and fauna that is found along that ridge. So it’s hot. It’s dry. And it has very
specific sandy soils that are found primarily
there, but not only there across the state of Florida. Now, you can see, though, as
we go into a hotter and drier Florida, that in fact the scrub
plum might do very, very well. This area in central Florida
with the optimal habitat is going to expand, as will
other parts of the state as well. So it’s difficult to predict
whether a species will do well or do poorly under
models of climate change. So we’ve made these
models and projections for, as I mentioned,
about 1,600 species. And this is a summary
of the plant diversity now, where the green
areas represent high species diversity
and the tan areas represent low species diversity. Now, as we model
the future and we look to a hotter,
drier 2050– I won’t show you the results
for 2080, but they’re even more extreme– we
see that there are species movements that are anticipated. In this map, the
green areas represent an area where there’s
an influx of species, and the tan areas represent
those where species will be departing from. So we see that there
will be species moving into the northern part
of the state, as expected for temperate regions in
the northern hemisphere. As climate gets
hotter and drier, species are projected
to move northward. But we also see some
increased movement southward into sort of the
Everglades region here, where it is
projected to be at least wetter
than where it might be in other parts of the state. So we see perhaps an
unanticipated bidirectional projected movement of plant
species, one set of species moving northward and another
set of species moving southward. Now, of course this
doesn’t take into account the fact that sea levels will
also be rising and affecting the habitats of Florida. There are some models that
predict that by 2050, there could be as much as a four
meter increase in sea level. Although most models are
more in the one meter, this is a map showing what
would happen with a four meter increase. In this map, all
of the gray areas will actually be underwater. So recall that this is one of
those areas where the plant species are projected
to move into sort of from the central
region of the state. And in fact, there will
not be habitat available at that particular
point in time. So this paints a not
very optimistic view of habitat possibilities
for the flora of Florida in the next several decades. And what we hope is that
this information can be used, perhaps by managers
of conservation areas, to help at least try to
augment those plant resources that we have and prevent against
the total loss of the species’ diversity. Now, I presented
this information from the perspective
of the plant diversity, but the same sort
of analyses could be conducted for any other
sort of group of animals, again using specimen
data from the museums. And we’re currently in the
process of collaborating with our colleagues
in the fish range to do similar sorts of
analyses on the fishes, and also with some
of our colleagues who study the butterflies
and moths of the state, to investigate what their
responses might be as well, particularly in
combination with what might be happening with the plants. Now, these tools and methods
are portable not just to other groups of organisms
in the state of Florida, but certainly this
whole methodology is something that can be used at
any level on a worldwide basis. And this map just shows
the biodiversity hotspots that have been recognized. And these could be targets for
where this sort of analysis could be done. Now I’d like to point
out that, however, to get to this point of
having massive amounts of data mobilized, we really need
collaborations– partnerships. And it’s not just
partnerships among scientists. Partnerships with
citizen scientists are actually leading
to new sources of data and new resources
that can be used for these sorts of questions. So an example of that
is a wonderful tool called Notes From Nature. And this is a transcription
tool that allows anyone to access a set of
museum specimens and provide the
transcriptions that are then associated with images. So for example, there
are four collections that have been posted
on Notes From Nature. And there’s a herbarium one, a
bug one, birds, and also fungi. And for whichever one suits
your fancy, you can specify. And then you’ll be given
essentially a label, and you’re asked to put in the
scientific name, the locality, the date, et cetera. And then that information then
gets fed back into the website. And then that
information is linked up with the image of the
specimen, and then is returned to the
herbarium of origin or the collection of origin. And this then allows
for many new specimens to actually go online
as specimens with data. So there are a
lot of things that can be done with specimen data. Most of these actually focus on
the locality, but many of them also focus on the date. And as I mentioned
before, there are a number of these different questions
that can be addressed, using a combination of
the information that’s provided just on that label. But what can we do with
the specimens themselves? Certainly there must be more
to the value of these specimens than simply the data
involved in the label. And so what I’d like
to do during the rest of my presentation is focus
on how these specimens can be used in genetics
and genomics, and also briefly in
ecology, and then wrap up with some
applications to conservation. Now, a huge effort in
evolutionary biology is the reconstruction
of the tree of life. And the plant branch
of the tree of life is certainly one of the
research foci of our lab. We’re interested in how
plants have diversified, what their evolutionary
relationships are, and what processes have led
to the vast diversification that we see. And certainly specialists
in other groups of organisms are likewise interested in
the same sorts of questions, but from the different
phylogenetic perspective. So you can think of this
as evolutionary history or phylogeny. And I like to use the
family tree metaphor where we have the
House of Windsor here, where we show
basically the reconstruction of the family tree. So this is
essentially what we’re trying to do when we
reconstruct the tree of life. Now, in fact Darwin’s
Origin of Species had a single figure in the
book, and that single figure was this. And this is essentially
a phylogeny, or evolutionary history,
of a potential putative group of organisms. Now, shortly following Darwin’s
publication of the Origin, other scientists grasped onto
this tree of life concept. And this is a rendering
by Ernst Haeckel, produced in 1867, showing
the vast diversity of life, summarized in this tree-like
figure with the plants on the left branch, the
animals on the right, and then various single-celled
organisms in the central part of this tree. Now, over a century or
more following this, most scientists recreated
evolutionary history primarily using the morphology,
or general attributes, of the organisms. But for the last
several decades, we’ve been using DNA
data to build these trees or reconstruct these histories. And essentially
all that’s required is to have a sequence of DNA
from each of several species. And we can compare
these DNA sequences for similarities
and differences, and use those
attributes then to build a phylogenetic tree, or
an evolutionary rendering of this historical relationship. Now, we can go from
this simple sort of tree to a much more complex one. This one includes a
couple thousand species. And this, again, is just
the tip of the iceberg. We are over here somewhere. This is the animal branch
on the outside of the tree. And I think that this
is a very humbling way to think of ourselves. We are no more
important than any of the other tips on this tree. We’re simply one of those tips. And then plants are here. So this is the clade of focus
for the next several slides. And I’ve expanded
this out a little bit to illustrate the green
plants, this branch of the tree of life. As I mentioned earlier,
there about half a million species
of green plants. They have a very deep
evolutionary history. They go back about
1 billion years. But most of the plants that
you’re most familiar with are the flowering plants, and
they fall within this clade here, which is a relative
newcomer in evolutionary time, originating, based
on the fossil record, about 130 million years ago. Now, we certainly know a lot
about the general features of the evolutionary
history of the plants, but there are many, many
details that are missing. And in order to fill
in those details, we can make great use of our
natural history collections. Now, these natural
history collections are not simply the
physical specimens of the organisms themselves. But in fact, in many cases
natural history museums, such as the Florida
Museum of Natural History and many others, also have
genetic resources, repositories or DNA banks that have
samples of DNAs or tissues that are also
available for research. And so we’re not limited
to the observations that we make on the specimens. We can actually go to
these collections of DNA and make use of
them as well as we start to try to reconstruct
the evolutionary history of these large
groups of organisms. Now I’d like to present
an example here, based on the work of one of my
graduate students, Greg Stull, because I really like the
way that he has developed an integration between
herbarium specimens, DNA data, and the fossil
specimens as well. So he’s using fossils, he’s
using herbarium specimens, and he’s using DNA,
all combined to try to understand the history
of this group of plants called the Icacinaceae. So here’s a picture of Greg. And the reason that he’s
selected this group of plants is because it has a
pan-tropical distribution. You can see its distribution
in South America, Africa, parts of southern India, and
then also in southeast Asia. And understanding how
these plants diversified, associated with the movement of
the continents in particular, has been particularly
interesting to Greg. The plants are woody vines. You can see here this woody
vine circling this tree trunk. And they have very
characteristic fruits. These fruits have very deep
reticulations, or networks, in them. And these make them very evident
in the fossil record as well. So this plate
shows fossil fruits from this group of plants from
about 60 million years ago. So because of the very
characteristic fruit features, the fossil record is
extremely valuable in this particular
group of plants. You can’t say that for
many groups of plants, but this is one particularly
useful attribute. So when you look at the fossil
distributions of Icacinaceae, this group, you can see all
of these little stars here. Those represent fossil habitats. So even though today the
plants are distributed only in the southern
hemisphere, you see a number of instances
of these fossils being present across
North America, Europe, northern Africa,
and also in Japan. So the fossils are really
valuable for his work, as are the herbarium specimens. But the herbarium specimens
are not only important as a source of general features. They’re also important
as a source of DNA. So these specimens actually
can be used as a source of DNA for doing molecular
work as well. So this shows a specimen
collected in 1955 in India. And Greg was actually
able, despite the sort of ratty appearance of this,
to get some very good DNA from this specimen. And in fact, it’s
possible to get DNA out of many herbarium specimens,
in some cases dating back over 100 years. This makes our Herbaria and
our other museum collections not just valuable as
resources for the label data and the morphology
of the individuals, but also as a
potentially huge DNA bank that is largely untapped. Now, it was for several
years a potential problem to use DNA from
museum collections because the DNA is often
slightly degraded– slightly to maybe very degraded. And in those cases, at
least using previous DNA technologies, it was very
difficult to make valuable use of that information. However, our current
DNA technology is all based on what
are called short reads. And so basically the
technology– and I think with this light
up here, you guys can’t see this too well. But the reads are very short. There’s just a small
number of base pairs. But we get lots
and lots and lots of copies of DNA sequences. And when these
things are generated, they’re lined up in
overlapping fashion so that even though you
start out with short reads, you can concatenate
them into long reads so that you get a very
long, intact DNA sequence. So what this means is
that we can actually use degraded DNA
because that’s all that this procedure
actually requires. And so our new
technologies are allowing us to make tremendous use
of our museum collections from a molecular perspective. So back to Greg’s
work a little bit. He’s using this information
from herbarium specimens to do genomic analyses
on plant specimens in this particular
group of plants. He uses the DNA
sequences to reconstruct the evolutionary history. And he’s just in the
process right now of analyzing the
data, so he’s not quite at this point of
having the tree put together. But I really like
the way that he’s pulling these different
resources together. And I think this is what the
future of our natural history collections will be, an
integrated opportunity to use morphology, paleontology,
and molecular data, all coming together to address particular
questions, ultimately allowing us to pursue in much more
detail the evolutionary history of life. And through doing
this, we can then understand better what the
processes are that have yielded this diversification. So I’d like to just
mention briefly an application to ecology. And that is that we can
also use our specimen data to make inferences about
the roles of species in the ecosystem. So this is particularly, again,
something that plant biologists are investigating. It’s possible, in fact, to take
our red maple example again, to take our herbarium specimen
and make some inferences, based on leaf characteristics,
about the role that that species might be
playing in a given ecosystem. And so now, through
image analysis, we’re starting to be able to
use herbarium specimens in yet new and exciting ways in
ecology that we previously were not able to do. And finally, if we
turn our attention to specimen data
and conservation, I’d like to return to this
area of Florida called the Lake Wales Ridge, located here in
the central part of the state. Now, this is an area
that is characterized by having many rare species. There are plants. There are birds. There are insects. There are all sorts of
organisms– lizards– that are endemic to this
one very narrow ridge. However, this ridge is
under tremendous threat due to habitat loss. The area has been converted,
first of all to orchards, then to golf courses, then
to retirement communities. And all of these sorts
of land use changes have altered the
native fire regime. And this is an area that
is very, very dependent on fire for rejuvenating
the vegetation. And so even those parts of the
ridge that are still intact have suffered because of having
this altered fire regime. So one of the most rare
species is this species called Ziziphus celata. And our lab, in
collaboration with groups at the University
of Central Florida and at Archbold
Biological Station, have been working for
many years to develop conservation and management
practices for the species. Likewise, there are many other
plant endemics, a few of which are listed here, that also
have some conservation plans underway. The problem is, you
can’t effectively conserve a large
number of species through independent sorts of
species-specific conservation plans. And so we’ve been
thinking about how best to scale up these
activities so that it’s not one species at a time. And we think that
one of the ways that we can perhaps
best do this– oops. Microsoft PowerPoint has
encountered a problem. OK. We’ll open that back up. I think the computer is
saying that we’ve had enough. We’ve only got a
couple more slides. Here we go. So if we return to our
analyses, using the label data to make predictions
about ecological niches and the future distributions
of these species, we could start to
think about doing this on a community level. So we could actually do
these sorts of analyses for all members– plants, birds,
lizards, insects, et cetera, all that occur in a
given area, and then do some sort of an
integrated analysis over time to hone in on perhaps
the best conservation strategies that could be used. So again, we have
projections for 2050 and 2080 for these plant species. But why not do this for the
groups of plants, particularly in a threatened area, and
also the other organisms that occur there as well? So I hope I’ve been
able to convince you of the great value of
natural history collections. Certainly they
maintain their utility for systematics and taxonomy. We wouldn’t want to
let Linnaeus down. We’re still doing the
same sorts of work in terms of specimens
and species descriptions that we were doing as a
community centuries ago. But of course,
these specimens now have taken on many
new sorts of values, ranging from their
resources as genetic banks, their opportunities for telling
us more about what might happen under models of climate change. They allow us to reconstruct
evolutionary history and make inferences about the
processes that have given rise to diversification. And they’re also valuable
as sources of data for conservation purposes. So with that, I’d like to thank
all of you for your attention, and thank my colleagues
at the Florida Museum, and at iDigBio, and a few other
folks who have contributed a lot to what I talked about. So thank you very much. [APPLAUSE] And I’m happy to take any
questions if anyone has any. Yes? This is a pretty
specific question, but I noticed over
there on those specimens and also on the sheet
that some of the dates– you have two different dates. So I was just curious from
a collections perspective, one of them is a collection
date, and the other one is– So a lot of times what
happens with a specimen is that as an expert comes
through the collection and uses that specimen
or studies that specimen, he or she will put an
annotation label on the specimen as well to say, this is my
name, I examined this specimen on this date, and I agree that
this is the correct species name. Or you might put on it an
annotation label that says, I removed a piece of this
specimen for DNA analysis, or I removed a piece for
biochemical analysis, or something like that. So if a specimen is
quite old and has been used a lot of
times, you can end up with a whole– you can
actually track the history of the use of that specimen. And of course, all
of that information would be great to
have online as well so that we have a record of
how a particular specimen has been used. Yes? I was particularly
interested in your map of the biodiversity hotspots. I think Greg did
that work, didn’t he? Your postdoc, Greg? So that biodiversity hotspots
map, that’s actually– I think it might be
World Wildlife. I’m not sure. It’s one of those organizations,
which was probably in the small print on that. I think it’s fascinating. And I realize it’s tied in
with projected global warming, but do you recall
the common thread? Because they seem to be
spread out, for example, around the US. I particularly focused in
on the Pacific Northwest. So what’s the common thread
that would make them– Yeah, so let’s– let me go
back, and we can put that up. Let’s see. I was going to ask
you to do that, but I wouldn’t have
asked you [INAUDIBLE]. Yeah. There we go. Yeah. Oops. There we go. Yeah, so a lot of times
it’s a combination of various geological traits,
climatic traits, things basically that allow for
diversification to occur. And so that’s why we see
things like– so yeah, there’s one in the
Pacific Northwest. And actually it’s
really the whole sort of western part of the US
that is included there. The California
Floristic Province is a highly species-rich
area in terms of plants and many other organisms. And that’s related to conditions
such as varied topography, varied climate, et cetera. And that yields
processes that can just lead to rapid diversification. We also see the same sort of
thing in the Caribbean a lot of times where there’s
geological activity and islands systems as well. Those often interact to
produce lots of species. So those would be just a couple
of explanations, I think. Yes? Do you work on any
carnivorous plants? And if so, how many? Oh, that’s a great question. So I had a graduate student who
worked on carnivorous plants, and he was particularly
interested in pitcher plants. So I had a picture
several times– I think you might have
noticed– of this pitcher plant on the left. So that’s one genus
of pitcher plants. But pitcher plants have
actually evolved multiple times in the whole history of
the flowering plants, in very unrelated groups. And so it’s an
amazing set of what we would call convergent
evolution, where kind of what looks
like the same structure originated multiple
times independently. And my graduate student was
interested in whether the genes involved in making
those pitchers were the same in these
very different groups. And he never quite solved
it, but he learned a lot about the genes that help
to make a pitcher out of a regular leaf. Can I go one more time? Mm-hmm. Are carnivorous plants very
common in the plant world? Well, they’re really found in
kind of four different places. If you think of
the plants as being this one great big
huge family tree, there are like four
sub-families in that family tree where you have
carnivorous plants. And then within each one
of those sub-families you’ve got various
types of carnivory. So sometimes you
get the pitchers. Sometimes you get things
like the Venus flytrap that actually closes
around some insects. And then sometimes you
get some other mechanisms that are either more active
or less active than those. But those are kind of two
of the most common ones. Yeah, thanks for your questions. Yes? Are any individual
natural history collections able to
prioritize saving, like storing DNA for some
of the older specimens, before a research
project comes along that will need that stuff? Because obviously this
timeline of decay is ticking. So I was curious. Are there initiatives– So unfortunately, the resources
for developing these DNA banks in the natural history
collections are limited. And so no one’s able
to have the sort of comprehensive collections
in their molecular collections that they have based on
their other specimens. So we’re always behind. What we’re hoping will
become best practices is that as people make new
collections of specimens, they’re also making new
collections for the DNA bank so that you end up not having
a backlog into the future. Certainly some
collections are going through their more
important collections and trying to save snippets. Particularly for plants
it works better, I think, than for most animals. A lot of the animal
tissues don’t hold up as well in
their preservatives as plant tissues do. But yeah, it would be–
with more resources, more collections
would be doing that. Yes? If I understood
correctly, you are thinking about
conserving ecosystems rather than individual species. I love the idea, but
how will it be done? Yeah, well, that’s, of course,
a really important question. I think we’re finding that
saving individual species is not probably going to work
unless we can save components of their ecosystems. And so the best way
to save anything is going to be through
saving larger areas of land so that we can preserve some of
the processes that take place within those areas. I’ve been pleasantly surprised–
so I’ve lived in Florida now for not quite 14 years, and
I’ve been pleasantly surprised at the general
attitude in the state toward preserving natural areas. So despite this 1,000 new
people per day moving there and this tremendous influx
of people and urbanization, there’s a strong regard for any
areas that are still natural. And so the state
government has been purchasing a lot of
these over the course of the last couple of decades. And so we’re hoping that
at least some of that can help in that
particular case. The problem is that the
patches are often very small. And whether that’s
enough to save anything I think is still
an open question. Yes? This is more an observation. You’re [? preparing ?] for
the date 2050 and 2080, and I would observe they’re
using tools that are probably less than 30 years old. And are you hopeful that there
are some new tools beyond putting things in the cloud,
or in other words, things you’re doing with DNA
that might [INAUDIBLE]? Or is it hard to make a crystal
ball that looks and says, I only wish we could
do such and such? Right, yeah. So that’s a really
good question too. I think it’s– I guess the
perspective that I’m having on all of biodiversity is that
we need to save as much as we can, not just in terms
of naturally but in terms of our specimens. And that will allow us
to maybe develop methods that we can use for
other sorts of work. But in terms of what’s
ahead, boy, I don’t know. Things have moved so fast
in the last few years, so it’s kind of hard to
imagine what might be next. Yes? I’m interested in the modeling. And since you have
a number of inputs into the model, and these
things change over time, what are your plans for updating
the models with new data that comes in? Because obviously
you’re extrapolating. Mm-hmm. So yeah, another great question. So what we’ve been
working on recently is developing models
that don’t use– so the way that these niche
models have worked in the past is that they basically rely on
a 50-year average of temperature for a given location. So if you have a
plant, and you want to find out what the
characteristics were at that point, you say, OK,
what year was that collected? And then there’s
a 50-year average that kind of is associated
with that point, to figure out the precipitation,
the temperature, et cetera. But what we’ve actually
done is say, OK, if this plant
specimen was collected in 1932, what were the
characteristics like in 1932? And there are actually
databases for the US that go back very far in
terms of precipitation and temperature, and
we can build the models based on what the
characteristics were for the particular year in which
the specimen was collected. And this actually allows us to
make the models much tighter than using these sorts
of bigger averages. So that’s one way that
I think that we’re becoming more able to improve
the accuracy of the models. Certainly we’ve done
these future forecasts based on several
different projections of CO2 emissions, an optimistic
one and a pessimistic one. And then each of
those has– I think for each of the optimistic
and pessimistic, there are like three different
additional categories. And so as those models and those
predictions for what the CO2 levels might be
become more resolved, we’ll also be able to probably
update the models as we go. So basically we’ve been
developing methodologies that allow you to plug
in your locality data and make these other
specifications, and then get your model
results out the other end. And those will be
usable regardless of what the actual
other components are. So that should make it easier
to do those updates that you’re suggesting. OK, let’s wrap this up. But before we give Pam
a big hand, please, there’s a little pop-up
display over here. For those of you that
have never actually seen herbarium specimens up
close and in person, you can actually take a peek. There’s more than you think you
can glean from these flattened and dried specimens than
you might believe, actually. But so otherwise, let’s give– [APPLAUSE]

2 comments

  1. This was a great presentation, until it turned into pseudoscientific government climate model BS that has been proven to wrong for the past thirty years.

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