Why genes come before species in Paint Rock

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What’s Alabama’s most valuable asset?

Its genes.

I don’t mean to be insulting, but I’m not really talking about your genes, or my genes, or the genes of any person you or I know.

I’m talking about the native genes of Alabama, the genes that have survived here for many millions of years, genes that often exist nowhere else in the world, genes found in Alabama’s fish, turtles, salamanders and mussels; in its rare sunflowers, carnivorous plants and mints; in its hickories, which are more diverse than hickories anywhere else on the planet.

 And for the past few weeks, I’ve been talking about the genes of Alabama elms. 

That’s because Alabama’s American elms aren’t like the elms in most other parts of the country. Most significantly, they’re different because they’re still alive in great numbers, while native American elms in places like New England and Michigan are all but wiped out by disease. 

Only recently have scientists woken to the fact that American elms in the southern tier of the United States must be very different than elms up north. 

American elms here are more genetically diverse, with more ways to genetically adapt to new challenges. The fact is, elms that have evidence of southern genetics now perform better up north than the elms that are “native” there. 

They may look similar, but the American elms north and south are virtually separate species – and it appears the trees from the Cumberland Plateau and coastal plain areas of the Deep South are closer to the foundation stock of American elms, and are the ones most capable of shaping the future of elms in America.

Strangely, though, Alabama almost let the rest of the country define our American elms out of existence. We let researchers who’ve never seen an Alabama elm determine what an American elm should be, based entirely on their research on elms in their Boston, Buffalo and Bloomington backyards. They weren’t aware that Alabama’s elms were so dramatically different because they had never sampled elms south of Washington, D.C. 

The bigger shame is that folks in Alabama never did either. 

What we overlooked with elms we’re in danger of overlooking with all of our Alabama genes, and the consequences of that are dangerous for all of North America. Scientists are increasingly aware of the importance of the few places, like Alabama, Georgia, northern Florida, the Carolina lowlands, where life survived for millions of years while life in much of the rest of the country was crushed by glaciers, drought and other severe impacts of climate change. Those places are refuges for genes that were lost elsewhere.

And it’s increasingly obvious that the trees and plants and creatures that now cling to the northeastern and north central states bet their future on life in a cold world, and are going to be particularly poorly adapted as the planet continues to warm.

The states of the Deep South, and Alabama perhaps more than any other, have the genes that the forests of Ohio, Pennsylvania, New York and Maine will need to survive this century.

The trouble is, we still don’t recognize the importance of our own Alabama genetics. Our universities have done a poor job studying them. And most of us have no idea what an important asset those genes are. Shoot, if we’re going to purchase trees for our Alabama yards, we’re more than likely going to import them from Ohio or Pennsylvania – while bulldozing the the native Alabama tree genetics that Ohio and Pennsylvania desperately need. 

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There’s one more thing that elms and other trees in Paint Rock should teach us about genes. Increasingly, we recognize that some of the most important Alabama genes aren’t prisoners to our species boundaries. Or maybe I should say that our often arbitrary species concepts may ignore the genetic differences that will be most critical to the survival of our ecosystems. We carelessly slapped species identifications on American elms, and in the process lost a half century of restoration potential. 

The evidence of our sloppy species concepts is everywhere. I am alternately appalled and amused by efforts to rid Mobile Bay and Delta of roseau, the giant reed (Phragmites spp.) that is so dominant in many areas there. It started, as so many of our misguided efforts do, because we let folks in other regions tell us what our species are. An invasive form of the giant reed from Europe had begun to take over marshes in New England. Their congressional representatives managed to get a big pot of federal funding to control it, and folks in Alabama realized, hey…we’ve got giant reed, too. Let’s get a chunk of that change.

But no one stopped to consider that while the European giant reed had come to North America only in recent decades, there are photos of giant reed dominating areas of Mobile Bay and Delta dating to the 19th century. There are accounts of the earliest French settlers building their houses of roseau in the early 18th century. 

To the casual observer – and that unfortunately included some scientists – the European plants and the Gulf Coast plants looked the same. And a full-scale eradication program was initiated to eliminate a plant that had been part of Gulf Coast life and ecosystems for as long as we had records. 

Thankfully, it wasn’t very successful. And a researcher willing to take the time to understand the plants in more detail realized that though they looked similar, the group of plants we dubbed giant reed or phragmites was in fact made up of multiple “haplotypes” – populations of plants with distinctly different genetic profiles. The populations from Mobile Bay were so different from the European populations, the researcher demonstrated, they needed to be seen as different species. Soon it became obvious to most biologists that the species even looked different, once it was recognized they were different.

But even if Karen Saltonstall had not made the case for new species, these plants were so genetically different we obviously needed to think about them and manage them as if they were separate species.

Unfortunately, our whole system of conservation is based on these kinds of crude species concepts.  We pretend that protecting sugar maples in New England is protecting sugar maples throughout North America. But thanks in part to the work we’re doing in Paint Rock, we now appreciate that the sugar maples of Alabama and the Southern Cumberlands have very little in common with the sugar maples of New England. As with elms, New England seems to have one genetic variant of sugar maple that slipped in behind the glaciers. In Paint Rock, we’re looking at the possibility that we have two or three “sugar maple” populations that are so different they can grow side by side and never cross – and it’s quite likely that all of them are not only genetically distinct from the sugar maples in New England, but also genetically richer.

Oaks, hickories, maples, elms, buckeyes, rhododendrons, ash, violets, fire pinks, sunflowers, silphiums – it’s like we just got off the boat with Columbus, and are seeing these species for the first time, and we’re working to identify the genetic strands that make them so different from plants elsewhere. It’ll be nice and useful to lump some of them together as new species. But in a place that is an ancient refuge for species, as Paint Rock and much of Alabama is, even individual trees matter, and we ignore the differences between individual trees at our own peril. That’s why we are identifying and following literally every individual tree over our 150-acre census plot.

At Paint Rock, we celebrate and honor species. And that’s why we take species with a grain of salt.

Elms and the species hounds

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Possible new oak species

Some might suspect we are species hounds at Paint Rock Forest Research Center, obsessed with finding new species.

Ed Wilson reminded us often that we should be. He wanted us to know every species on the preserve, including the 80 percent of species that none of us know.

And we seem to be doing that, a small piece at a time. We’re in the drawn-out process of unravelling multiple species mysteries that could result in newly named species of oak, maple, buckeye, dogwood, azalea, hickory, violet…the list grows year by year. We hope that list will soon include insects, vertebrates, fungi, cave life, aquatic life that no one has ever heard of before.

Some might even accuse us of being deliberate “splitters” – a label that some botanists lob at those they feel are just trying to devise new species based on “minor” character differences that don’t matter. If splitting involves having to learn a bunch of new Latin names, there’s usually a snarl attached to the name-calling. 

But what’s more important to us than finding new species is beginning to understand what a species really is, conceptually and individually. 

Oh, you thought we already figured that out? Well, no.

In fact, scientists around the world are rethinking conventional species boundaries. A giraffe, we now know, isn’t just a giraffe. It’s a complex of four very distinct species, with nine different subspecies that are all on separate evolutionary paths. Why did it take so long to understand that? 

It’s partly because we’ve long had a very crude and cursory way of looking only at the mostly obvious physical characteristics where species are concerned. But giraffes are more than just long necks, and now we see quite clearly that there are species of giraffe that are not only genetically distinct, but also (on closer inspection) different physically, with different adaptations to the massive differences in habitat and communities across Africa. In the face of changing climate and human impacts, the future of giraffeness may depend on recognizing and preserving all those species and subspecies.

The same reckoning is happening here in the Southeast. For years, we were content with hand-me-down descriptions of species, often from elsewhere in the country where species diversity was less rich, and perhaps a bit easier to describe and master. 

I continue to be amazed at how simplistic our notions of southern species once were. Who can look at the leaves and fruits of Southern shagbark hickory, and not immediately see how different it is from Northern shagbark? Who could ever have possibly thought pagoda oak and Southern red oak were the same species?  How could anybody mistake Cumberland hill cane, with its distinctive short habit and deciduous leaves, for the “giant” evergreen cane of our river bottoms? And yet, until the past few decades, these plants were all lumped together and their conspicuous differences largely ignored.

Species definitions have always been shaped by our ability to see the differences in things, and by our willingness (or not) to see the difference. Foresters in the early part of the 20th century didn’t have the tools to easily see the genetic differences in trees, but when a dozen species of red oak were going to be mixed at the mill and bring the same price, they didn’t see much need to discern them either.

A new generation of taxonomists, like Alan Weakley and Bruce Sorrie in North Carolina, Dwayne Estes, Robert Kral and Jayne Lampley in Tennessee, Brian Keener and John Freeman in Alabama, and Jim Allison in Georgia, have challenged us to look again at familiar groups like hickories, oaks, violets, wild gingers, trilliums and many others. 

What we now see are not just subtle distinctions, but distinctions that can make a world of difference. The difference may not be easily and immediately discernible by leaf shape, or bark, or even flower or fruit. But it can sometimes be easily parsed in the distinctive genetic makeup of each new species.

That was the great surprise with the American elms of the Cumberlands. They, along with elms from a few other spots in the Deep South, were so genetically different from American elms up north they couldn’t effectively interbreed and share genes. They were reproductively isolated, and apparently had been for millions of years. There’s no more firm dividing line between species than that. The truth is, we still don’t have a key that makes it easy for us to tell them apart in the field. But why should that have ever mattered to the elms, as they were shaping their separate evolutionary paths? 

More importantly, why should any of this matter to us? If there’s no significance to finding these new species, then we’re all just collectors, with our little species trophies sitting on our shelves like bric-a-brac.

But the recent discovery of a potentially new “hidden” American elm species demonstrates why it’s so important to re-examine what a species is, conceptually and individually. Those hidden species may have extraordinary resistance to the diseases that have wiped out elms across the rest of the country. In large measure, the radically distinct Southern/Cumberland version of American elm was “discovered” not because it looked conspicuously different, but because a few of its progeny were so conspicuously resistant to disease. Recently described species within the white ash group may have characteristics that help us better respond to the threat of emerald ash borer. Still largely unexplored differences in the butternut group may help us understand why one of North America’s most delicious nut trees is still thriving in Paint Rock, even as it’s near extinction most everywhere else. 

Call us “splitters” if you like, but when splitting makes a difference to the future existence of the elm genus, we’ll take that as a compliment.

Each time we refine our ideas about what an individual species is, we also can sharpen our idea about what a species should represent. And it may be we need a much more refined language of species that truly captures the broad and often very important differences between populations and individuals, even when they don’t fit the classic definition of separate species.

Once again, Paint Rock and the Deep South should be the testing ground for these new concepts. We’ll talk about that next time.

The abnormally normal American elms of the Cumberland Plateau, and why they’re so important to the future of elms.

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How is it, when millions of native elms died from a virulent disease all across the county, elms in the South pretty much laughed it off?

Dutch elm disease has been catastrophic for American elms trees in
much of the northern tier of the county. And because so much of the
advanced research on trees is focused on northern forests, most folks assumed that American elms in the rest of the country were dying at the same rate.

Only in the last few years did scientists begin to scratch their heads
about the persistence of southern elms, which were thriving in spite of the fact that Dutch elm disease had clearly invaded here as well. 

For years, the few scientists who paid attention thought that trees were surviving here because the disease and the insect that carried it were less common in the South.  But there were problems with that hypothesis, including the fact that the invasive European beetle that carried the disease was producing three generations per year in the South.

And then there was the curious case of a few horticultural clones of
American elm that thrived and were disease-immune wherever they
were planted, even in the core of the area devastated by Dutch elm
disease. When researchers at the National Arboretum began studying these trees, they discovered they had an odd number of chromosomes. Because these trees were nursery stock, no one was really sure where the parents came from. But it was pretty clear that at least one of the parents of these trees was very different from any American elm ever studied.


And so for the first time – and just a few years ago – USDA researchers began to test elms from farther south. The American elms north and south may have looked alike, but molecular testing showed they were so different genetically, they might as well have been different species.

For decades, scientists assumed that all American elms had an extra set of chromosomes. Chromosomes pretty much drive the genetic inheritance of all living things, and “normal” creatures (including almost all humans) carry only two sets of chromosomes, one from each parent. But all the American elms tested in cities like Boston and Minneapolis had four sets of chromosomes – twice the normal number. It may sound kind of freakish, but this happens to plants and animals. It cansometimes result in a fatal defect. With plants, however, those extra sets of chromosomes can provide some benefits, even helping a plant grow faster or bigger, or withstand competition or severe conditions.

But when scientists finally got around to testing American elms in the South they were in for big surprise. Many of those elms were “normal” diploids, with only two sets of chromosomes. Trees from the Cumberland Plateau – which stretches from Birmingham and Huntsville north through Kentucky and southernmost Ohio – stood out as being consistently diploid. It’s probably no coincidence that these trees were in the heart of elm diversity in North America, and represented an area where DutchElm disease had been much less troublesome.

What was going on?


It doesn’t make sense unless you understand the repeated changes in climate that brought glaciers as far south as Washington, D.C. Those glacial outbreaks occurred frequently over the past several million years, wiping out forests (and everything else) in their path. The most recent was one of the most intense, and it happened only about 50 forest generations ago. Only forests in warmer refuges close to the Gulf Coast or the southern Atlantic survived.

When glaciers retreated as climate warmed again, they left a freshly
plowed and virtually lifeless landscape. Trees like the American elm
rushed in to take advantage of all that fertile mud. The trees that got
there first had a big advantage. Once they took hold, they dominated, and it was more difficult for others to follow. There’s a downside to that. Scientists call it the “founder effect” – the populations of trees that took hold in the northern states typically carried the genes of only a few parents. They were in essence in-bred compared to trees that had avoided the glaciers farther south.

There was another issue that may have been just as important. The
American elms that could best take advantage of the land rush for the northern territory were obviously polyploids – trees that had a defect that caused them to have extra sets of chromosomes. Those extra chromosomes probably helped the trees cope with the frigid conditions on the retreating edges of the glaciers. Those polyploid changes may have even allowed the trees to reproduce and grow more quickly.

Now, however, we know there was a cost. Those polyploid trees up
north had cell walls and vascular systems that seem to have made them more susceptible to Dutch elm disease. Because their genetics were so limited overall by the founder effect, it’s also likely that they didn’t have the genetic bench that would allow them to

adapt to new diseases. And as is the case with many polyploids, their ability to trade genes with other elms was likely compromised, which further limited their ability torespond to disease.

This recent discovery of two distinct types of American elms has only led to more questions.

Are the diploid “American elm” trees from the Cumberlands the “original” American elm that never made it up north? Are they in fact an entirely new species of elm? 

Because trees with extra sets of chromosomes can’t easily mate with trees that have the normal number, these two elm groups are sexually isolated – one of the majorprerequisites for determining new species. University of North Carolina taxonomist Alan Weakley notes that these two groups of American elms appear to have been on a different trajectory for some 15 million years.

And if difference in chromosome number is the primary reason for
disease resistance of the Cumberland elms, then why are so many other elms in the south – regardless of species or ploidy levels – apparently resistant to Dutch elm disease?

And by the way, where’s the borderline between the “normal” southern diploids and the polyploids? Do Paint Rock’s American elms belong to the older diploid group, or to the more recent polyploid group that pioneered up north? Or do the forests of Paint Rock actually support both?

The truth is, no one knows. The study of Southern elms – which
apparently represents the foundation of elm inheritance in eastern

North America – is still in its infancy, and only one tree from Alabama has ever been sampled for its DNA. Let me repeat: Only one tree. In the heart of elm diversity.

Given what’s at stake – the future of American elms throughout North America – don’t you reckon it’s time we started working on that? I get excited about the possibility every time I walk up the first hillside in our census plot. Within a hundred yards, four species of elm are common, including American elms that may hold the key to Dutch elm disease resistance nationally. We’ll soon have mapped the precise location of thousands of elm trees on our 150 acre forest dynamics plot.

It’s also important to note that this isn’t just a story about elms. It’s really a story about our poor understanding of species, and even what a species is, and about how the whole country suffers when we undervalue the genetic diversity of the Southern forest. That’s what we’re wrestling with here at the Paint Rock Forest Research Center, and we’ll visit that subject in more detail next time.

Paint Rock’s “undead” elms and what they tell about the importance of our research

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Paint Rock’s elms aren’t supposed to exist. Or at least, they’re supposed to be very unhappy and all near death. But the truth is Alabama’s many species of elms are all about as happy as trees can be in a world like this one. They’re mostly thriving. And if you understand why they’re defying so many assumptions, you’ll get a clue how important Paint Rock will be to the future of Eastern North America’s forests. Scientists started writing off the future of Alabama elms almost a century ago, when Dutch elm disease began wiping out elms at an astonishing rate in major cities in the northern half of the country. This introduced disease took a small bite out of elms initially, and then seemed to mutate into something even more deadly by the 1950s.

The disaster was painful and conspicuous. American elms, one of the species most susceptible to the disease, was also one of the most widely planted trees in the nation. Elms lined the streets of Boston, Philadelphia and Minneapolis the way live oaks now line so many streets in Mobile. Their architecture created high tunnels over America’s new neighborhoods, and they made the endless lines of houses and the fresh concrete seem welcoming.

But by the 1970s, literally millions of trees were dead or dying, tree after tree, down all the streets they were planted on. The death was so catastrophic, and the falling limbs so threatening, cities pre-emptively removed the remaining elms, and discouraged folks from ever planting them again.

And because Alabama too often mimics its northern neighbors without thinking, Birmingham, Huntsville and many other Alabama cities followed suit, virtually banning native elms from city streets. This was particularly harsh, because cities like Huntsville and Birmingham were known not just for their American elms, but for their many other species of native elms, like the magnificent September elms, which were unheard of farther north.

And to this day, urban planners and foresters will look at you like you you’re crazy if you suggest replanting our cities with native elms. They’ve read all the books written up north: Surely these elms would be a disaster. To add insult to injury, nurseries have unleashed a host of really weedy, brittle and just plain obnoxious elms from Asia and Europe in an ill-advised attempt to “replace” our native elms.

It’s too bad we don’t know as much about our own Alabama forests as we know about the trees in Boston. Because American elm is abundant, and at times almost weedy, in Alabama forests. There are tens of thousands of tall and healthy specimens in the Mobile-Tensaw Delta, and on the banks above. Elms still grow tall at Elm Bluff near Selma and at Elm Grove near Birmingham, and there are four or five native species of elms abundant in the Paint Rock Research Center forests, which may represent the greatest concentration of native elm species in North America.

Sure Dutch elm disease shows up occasionally, just to let you know it has made its way to Alabama. But most of our trees never show any symptoms, and death from it is so rare in our forests, even those of us who spend a lot of our time looking at elms will never see it happen. So how in the world are all these elms continuing to do so well in Alabama, when they died by the millions in so many other places in the
United States? Well, there’s an important story there about the unusual and ancient genetic heritage of our elms, and a lesson in why it would pay us in Alabama to understand where we are from. And it helps explain why our research at Paint Rock is so important to all of North America.

What in the world do you do there at Paint Rock?

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We’re doing more than any organization our size should be capable of.

We’ve gotten it done because of our partners like founding members and UCLA Distinguished Professors Stephen Hubbell and Patty Gowaty. Because of our long and expanding relationships with The Nature Conservancy and Alabama A&M University, with the Student Conservation Association and Americorps, and with research partners at University of Alabama, Auburn, University of West Alabama, Yale and elsewhere. We’re getting it done because our board members roll up their sleeves whenever we get stuck in the mud, and because of the growing support of our local communities and legislative delegation. And we hit above our weight because of you, and your support throughout our fledgling years. We’ll need your support more than ever

in the coming year, as we build on the foundation we’ve laid. But seriously, what in the world are we doing here in Paint Rock?

Here’s a sample:

The FOREST CENSUS

Teams from the Research Center and Alabama A&M have labeled more than 40,000 stems in some 75 acres of the forest dynamics plot. That’s about 60 football fields worth of trees — the scale of it is hard to imagine until you see it. As we climb through the next 60 football fields worth of trees, we anticipate we’ll have mapped and tagged close to 100,000 trees. 

Thanks to the work this year of Juliana Sandoval and our Student Conservation Association research interns, we are very close to the halfway point in our forest dynamics census — measuring, tagging and mapping every stem larger than a pencil. Helen Czech of Alabama A&M is just a few steps behind, nailing the identities of all the trees. 

And thanks to Dawn Lemke and Alabama A&M, the first 50 acres of the plot is already being prepared for its RE-census in 2024 —that’ll be the first of 10 or more re-census efforts over the next 50 years. Those recurring censuses are the key to understanding the dynamics of the forest, its growth rates, its ability to capture carbon, its response to changes in climate and carbon dioxide. All the things we need to know to protect the future of our forests. But even as we complete the first census on half the plot, a few astonishing things are already very clear:

— The tree diversity on this site exceeds any other forest dynamics plot in the temperate world — more species than any ForestGEO site in North America, Europe or the or the non-tropical zones of Asia. Forest dynamics plots in places like the Pacific Northwest, Yosemite, Florida, Indiana and Harvard Forest in New England don’t come close to a proaching the kind of exceptional diversity we’re seeing here.

— The truth is, we don’t know precisely how many species we actually have because so many of the trees we’re looking at defy any current species definition. That’s why we’re working with Morton Arboretum in Chicago, Samford University in Birmingham, University of West Alabama, University of Missouri, University of North Carolina and Austin Peay University to try to understand what these species are. It appears we’ll be helping to redefine the sugar maple group, and it’s very likely we’ll all need to learn the new name of a very large and prominent Cumberland oak. If only we had the time and funds — we’d be looking more closely at some of the unclassifiable hickories, dogwoods, azaleas, buckeyes and other species we’re seeing on site. We simply had no idea we’d encounter so many surprises in one place.

The RESEARCH INTERNS

You’ll shake your head when you see it: The census is obviously a lot of work.But just as importantly, it’s a training ground for a new generation of scientists, of all backgrounds, from all over the state, the country and the world. Most of our research interns would never have had a chance to even encounter such a diverse forest system. But these interns live in it and live with it for months at a time. For those who have only seen nature through a microscope or on a cell phone, It changes the way they view the world. This year, we’ve introduced 8 research interns to the science and wonder of the Paint Rock Forest. In the coming year, we hope to introduce even more — and we’re raising the funds to enhance their educational experience, by allowing them to develop their own research interests outside the census itself.

The SHORTLEAF PINE SEED PROGRAM

In the burlap bags stored in our barn, some 35,000 shortleaf pine cones are releasing their seeds. With the help of our interns, a National Fish and Wildlife Foundation grant and many great partners, we collected those cones this fall in an exhausting effort. Nearly as we can tell, that’s the first time in 70 years or more that shortleaf pine seeds have been collected from the Cumberlands. We’ll do it again this year, only at a larger scale. And it’s just in time, because the shortleaf pine ecosystem — a savanna-like ecosystem rich in rare plants

and animals found virtually nowhere else — is among the most endangered systems in the Southern Cumberlands. 

These are the seeds of a revival not only for the landscape, but for a way of a life that was so important to the Cumberlands. By the time, we’re done, we hope to have produced enough seedlings to restore tens of thousands of acres of shortleaf pine, and in the process create a restoration industry for Paint Rock Valley that will provide seeds and career opportunities for decades.

The CAMPUS

The Paint Rock ecosystem’s unique character and its biological splendor is shaped by its immense size — covering some 450,000 acres — and its limited access. But the lack of access that left many ecosystems here relatively intact has also limited research into those systems. That’s why the Paint Rock Research Center campus is so important to our efforts.

This past year, we finalized the long-term mortgage on our central campus, which includes 10 acres and more than 7,000 square feet of residential, lecture and research space. We’re now developing a strategy to acquire an additional 3500 square foot home and 10 acres adjacent. They’re impressive buildings, wiith details and comforts most researchers aren’t used to. But that’s the point. We want to attract researchers from around the world. And we want them to say, as did David Attenborough’s Silverback film crew after filming here for a month, that this is the best residential and research facility they’ve ever worked with. Demand for space next year and our rooms are filling up. We’ll need to expand as soon as possible.