For this podcast, I spoke with David Neale, who has devoted his career to forest trees. I had interviewed him for a story in Nature Methods about research organisms called Model organisms on roads less traveled. But, as usual, I feel there is so much more to share about his work.
He told me about redwoods: there’s the coast redwood (Sequoia sempervirens) and the giant sequoia (Sequoiadendron giganteum), which grow in California, and the dawn redwood (Metasequoia glyptostroboides), which grows only in China.
He initiated the Redwood Genome Project that was funded by Save the Redwoods League to sequence and assemble the genomes of the two trees that grow in the United States. Note to self: I should check on whether the dawn redwood genome has been sequenced. The work was completed with computational biologist Steven Salzberg and colleagues at Johns Hopkins University
You can listen to the podcast here and it's also on streaming services. A transcript is pasted below.
(Credit: Max Forster @maxforsterphotography, courtesy of Save the Redwoods League.)
Note: These podcasts are produced to be heard. If you can, please tune in. Transcripts are generated using speech-recognition software and there’s a human editor. But a transcript may contain errors. Please check the corresponding audio before quoting.
Conversations with scientists: A conversation with David Neale, professor emeritus of the University of California Davis, and director of the Whitebark Pine Ecosystem Foundation.
I'm a forester, I've spent my entire career doing genetics of forest trees. I'm a kid who, you know, knew a very, very long time ago, I'd spend his life working on trees
Hi and welcome to conversations with scientists, I'm Vivien Marx. I interview many researchers for my stories and these podcasts are how I present more of what I hear and find out. Today, please let me introduce you to Dr David Neale, who is, as you've just heard, a forester. He cares about trees in particular the redwoods.
David Neale [0:40]
People use the term redwoods, generically, it could be any one of those three. Coast redwood, Giant Sequoia, and then a tree from China, Dawn Redwood.
Among the many trees David Neale has worked on, also with collaborators, are two of these trees. The giant Sequoia that grows in the Sierra Mountains, and the Coast redwood, which grows along the coast, in California and Oregon.
(Credit: Roy E. Williams II, courtesy of Save the Redwoods League.)
David Neale [1:05]
There's a very unique thing about coast redwoods. Sequoia sempervirens. It's a polyploid. In fact, a hexaploid. Ouch. You know, you and I are diploids we have you know, two sets. Some things are tetraploid. Coast Redwood is very unique among conifer taxa. They're all diploids except for something happened with this coast redwood it's a hexaploid. And that's One of the motivations, a small non applied justification for sequencing the genome is to figure out how and when this happened.
So in, you know, there are different ways you can get there, you can just, you know, you know, copy yourself and you know, where there were two there become four, or you can hybridize with something, right. And angiosperm species do this. ubiquitously, you know, that the angiosperm clade of plants is full of polyploids. But on the gymnosperm side, it's very, it's quite rare. And then, specifically the conifers, it's redwood is actually unique. And, you know, again, you know, what is what does that give this tree? You know, it probably doesn't explain why it gets to be 350 feet tall. But, again, there's something going on there with that tree. All kinds of interesting things.
David Neale was up until recently at the University of California Davis, where he worked on forest trees and forest tree genomics.
I'm retired actually. My official title for UC Davis is distinguished professor emeritus.
He is now director of the Whitebark Pine Ecosystem Foundation, which is about research related to whitebark pine ecosystems and also support restoration and management of these trees. And he is focused on educating the next generation of forest researchers.
David Neale [2.55]
I'm just enjoying trying to essentially empower the next generation, you know, nice. That's really what I have the most passion for is enabling, you know, with contacts that I have and, you know, having the experience of doing things to try to mentor young people and attract them into working on these organisms. I'm a kid who, you know, knew a very, very long time ago, I'd spend his life working on trees. And that's what I want what I'll continue doing in the retirement.
Empowering others to work on trees involves for example knowledge that comes from the genomes and the ecosystems the trees live in. Knowing tree genomes can help to support tree ecosystems research and understand the impact of climate change on these trees. It's his view that forest trees are a great way to study longevity and adaptation.
He may be retired but as is true for many researchers retirement just means continuing science in other avenues. David Neale's days are packed with science.
It hasn't stopped. I can tell you about a proposal I've been writing just before this phone call.
He doesn't stop indeed. While at UC Davis, one of his big projects on which he collaborated with others was to sequence and assemble genomes of many tree species including coast redwood and the Giant sequoia. That particular project was completed together with colleagues at Johns Hopkins University and other universities and was funded by the non profit Save the Redwoods League.
Knowing the genome sequence can help to understand these trees better.
Sometimes researchers study so-called model organisms, which are considered a model for many other organisms.
Historically, in the 18th and 19th century and this is based on writing from University of California biologist Rowland Davis as evolutionary mechanisms were increasingly appreciated, biologists studied nature to work out patterns that help to explain diversity, complexity and how organisms develop.
In the 20th century, genetics emerged and led researchers to shift their focus to genetics. They started with a few model organisms such as corn in 1900. Other organisms followed: mouse, fruit fly and others.
As genomics advanced geneticists started to work on many more organisms than these models and were no longer confined to these models, but it is true that much research has been done with these model and much research still takes place on these models.
In the 21st century and this is from Rowland David, biologists are going back to studying diversity and complexity in the natural world.
In the plant world, Arabidopsis also called thale cress, became a model organism and is well-studied. Forest trees have not been classic model organisms. Here's David Neale:
David Neale [6:00]
They have never been thought to be models for anything. You know, because of the difficulty and working with these organisms. They're long lived, you know, they're not easy to make, you know, for genetics to make crosses, self pollinate. And the conifers specifically have these very large, large genomes, all of which, you know, are sort of the opposite of all the attributes of something like Arabidopsis, you know, that has an extremely small genome, can easily be clonally propagated, crosses can be made by graduate students, and, you know, two weeks in a greenhouse, all this kind of stuff.
These trees large genomes that was a challenge he wanted to take on. David Neale approached Johns Hopkins University researcher Steven Salzberg, a computational biologist, about sequencing and assembling tree genomes.
David Neale [6:30]
There's certainly a challenge for the genome assembly people to assemble a 30 gigabase genome versus a one gigabase genome. You know, when I first called Steven, about this, he said, Well, that sounds interesting. But I don't know if we can do it or not, but we'll try.
It was just important to David Neale to make headway on these complicated genomes.
David Neale [7.15]
I was the, the guy who was, you know, sitting around for a long time trying to figure out how to how we might sequence conifer genome of its large size and complexity. It was an economic challenge as well, you know, back in the first generation sequencing era, you know, the, the cost of it would have been prohibitive.
So that held it up in people's minds, you know, was just off the table because of the costs. But second generation sequencing sort of change that picture a little bit. But then came the issue of the complexity, you know, huge amounts of highly repetitive DNA, that would then make assembly. Very, very difficult. But we said, well, we're going to try it anyway.
Yeah, so that held it up in people's minds, you know, was just off the table because of the costs. But second generation sequencing sort of changed that picture a little bit. But then came the issue of the complexity, you know, huge amounts of highly repetitive DNA, that would then make assembly very, very difficult. But we said, well, we're going to try it anyway.
He landed funding in 2010 from USDA, the US Department of Agriculture.
David Neale [8.00]
But I was doing the politicking for many years before that. And, you know, lots of different, you know, that's what scientists do, you know, to try to get one of the funding agencies to step up and do it. And finally, the USDA did. It was a fairly bold decision on their part, to put up the sum of money that they did at the time. But they did and we were successful.
One aspect that fascinates David Neale about long-lived forest trees is their adaptability.
David Neale [8:25]
For me, and my entire career that is really, I won't say fundamentally unique but quite unique about long live forest trees, is their ability to, you know, to adapt to the environment.
When animals when it gets hot in the kitchen, you move with annual plants. If you don't like it, you reproduce and spin offspring and send them out to the environment where they can find a successful place to live. I'm writing a proposal this afternoon to sequence the genome of bristle cone pine. I don't know if you know this tree, that it's a rare pine tree found in California. They're the oldest living organisms on Earth, these trees will live to be in some cases, 5000 years old. Wow. So there's some there must be some fundamental knowledge about longevity, and the ability to, you know, live through multiple environmental epics.
Some plant biologists think all that you need to know about plants can be found out by studying the model Arabidopsis.
David Neale [9:35]
I remember having a very contentious argument with at a meeting hosted by some Arabidopsis geneticists, telling me that everything can be learned about adaptation to the environment and plants through Arabidopsis. And I said, you know, I don't really think so. You know, I think there's something going on in these things that can live for long periods of time, and changing in different environments, that needs yet to be discovered. So, of all the things that I think are of profound, fundamental interest, that's, that's foremost in my list, and why these organisms can serve back to your point can serve as models for adaptability and longevity. In certainly in the plant kingdom, the other annual short lived organisms, I don't think are going to be as informative.
Much funding has gone into Arabidopsis research. I wondered if Arabidopsis was really more exemplary than forest trees. It's often a financial logic to why one organism is chosen over another as a model system. Here's David Neale.
David Neale [10.45]
Certainly in the early days, you know, when you know, people like Elliott Meyerwitz, and others, you know, advanced Arabidopsis as a model for the study of plant genetics. You know, just like Drosophila, you know, you pick one organism, and you invest heavily in it, and nothing should be taken away from the knowledge that was accumulated. And the, you know, going back 20 years, the ability to sequence a genome was non-trivial. And it would not have made sense to begin with sequencing a very large genome of some kind, just because of the cost and complexity.
So, all that made sense 20 years ago, but technology has advanced rapidly, to the point where, you know, how much do we really need a model? You know, I think the playing field is very level. Yeah, technology leveled the playing field.
Now, let's go out there, and pick the organism that's going to best answer the biological question that we have in mind, not make one organism try to answer every question.
Instead of model organisms and Alejandro Sanchez Alvarado who directs Stowers Institute, has pointed out to me that one should say research organism. Efforts in some labs on research organisms including David Neale's have been about focusing on the biological organism of his interest: forest trees.
David Neale [12.15]
I'm not a question-driven individual as much as an organism. I'm a forester. But my organism of choice, I think, has a lot to offer in terms of discovery of basic knowledge related to adaptation and longevity, that other more advanced systems, or traditionally more advanced system, Arabidopsis , maize, would not provide.
David Neale has been the principal investigator on genome projects devoted to the coast redwood and the giant sequoia and had been the principal investigator on the first conifer genome sequenced with funding by the US Department of Agriculture. The idea About sequencing and assembling genomes is to make it possible to compare these organisms.
David Neale [12:55]
This is where the field of comparative genomics comes in, you sequence something very long lived, and then you sequence something short lived. And, you know, you look for the differences, you know, what's here, or what's not in an organism, not so much coast redwood that's long lived, it can be 2,000 years old.
But this other organism, I was talking about bristlecone pine that lives to be 5,000 years old, is sort of a compelling reason to do that genome. So yeah, the genome is just a necessary resource in biological science these days, you know, you can do things without it, as we always did. But if you have one, things go a lot faster and better. If you have a parts list, if you will. I'm sure there's some that you're studying.
And with that genome and with that parts list one can venture to study questions such as the impact of climate change. Trees do not have legs so they can't pick up and leave when the climate changes. They need to adapt.
David Neale [13:55]
That's the big driver, and a lot that we're doing. We know that these trees are going to have to adapt to a changing climate, and what's it going to take to do it? And you'll see this in redwood, our giant sequoia, white bark pine and all these genomes, that's sort of a driving expectation is understanding the nature of adaptation under a changing climate. Because these, again, these things can't move. And it takes a while for them to disperse naturally. Sure.
So, you know, you know, up comes this idea of assisted migration, you know, people who reforest populations might say, Redwood is going to move north. And, you know, what are the what's the genetic composition of trees that would survive in those environments that might not survive in more southerly environments. So that's, that's the kind of applied information that we're trying to provide resource managers.
As climate changes, trees and the ecosystems to which they belong change, too. It's about whether or not redwoods can survive and where. Perhaps they might thrive, say at a different latitude, and there are many other questions.
David Neale [15:10]
That's right, you know, or, you know, all kinds of not just latitudinal change, but, you know, all kinds of ecological complexity. A big thing that we study, and a lot of these trees is adaptation to drier environments, you know, that, you know, with climate change, the moisture may become very limiting for some of these organisms.
And some of these trees, some of these genotypes within a species are better adapted to drier environments than others. You know, just like, you know, the genetic variation that exists in human populations, some of us are gonna get cancer, and some of us are not, you know.
Some of us can run fast and some of us can't. There's a genetic component to all of that, while we're looking for the those same genetic differences among tree populations, and using that information, proactively in reforestation restoration programs.
Science doesn't simply translate into managing ecosystems all on its own-- it takes people who actively help with that translation.
David Neale [16:10]
For a lot of these genome projects that USDA one that I mentioned a minute ago, we had a very large, significant component of that project, one full time PhD person, just doing outreach, you know, conducting workshops, oh, wow, nine resources. You know, yeah, to get it out of just academic refereed journal format, and make make it understood to the people who actually have to implement this knowledge on the ground. And so yeah, we do that with all of our projects.
When speaking with those who will implement policies and approaches, he comes across many different reactions.
David Neale [16.50]
Like everything else, it's mixed. You know, some people endorse enthusiastically, that, Wow, great. This is interesting. This is a new tool for my toolbox. And then on the other end of the spectrum, there is someone who says, oh, boy, I gotta learn something new and do something different. And that's threatening me and my security and my current job. And this is all a bunch of junk. And let's not do this.
Developing resources is for people who are managing forests and it's for people studying forests and a to foster the next generation of forest researchers and forest managers. This is a point David Neale makes with funders. He has also looked to a non profit Save the Redwoods League--to try to get funding help to be able to sequence and assemble the genomes of the coast redwood and the Giant Sequoia.
David Neale [17.40]
You point to a very important point that I make with the funders often is that, hey, we've got to develop these modern resources, so that we can attract good young people to working on them. Because they have their own practical needs, they've got to get a degree they've got to publish, they gotta get employed, they got kids to feed. And if you can see a path to doing that on Arabidopsis, even though you would love to work on redwood, because you walked among those trees, and they're a lot more interesting to you.
And I see this all the time, young students will have to choose the practical path that they can see, you know, an easier way forward in terms of publication, and then all the downstream things that you know, you gain from that, versus working on something that's maybe a little bit higher risk, scientifically. So that was a justification that I used with this redwood project was son was funded by a nonprofit organization in California called Save the Redwoods League. And that was an argument I made to them.
I said, Listen, we got tons of young people here in California who would love to work on this organism, but they're not. Because they don't have the tools. And if you can raise the money I can get, I can build the tools, and they will come.
Vivien And what he means by tools he includes includes genome information
Well assembled, well, annotated genome, you know, has become an essential tool in biological science. I think.
He hunted high and low for funding and possibilities and kept discussing for example with Save the Redwoods League.
It was all just a discussion. And they surprised me one day and call me up and said, okay, yeah, we got the money. Let's go.
Redwoods are majestic trees, I personally have never seen one in real life but the photos are astonishing. And so is the history of these trees.
95% of the old growth redwood trees were cut down.
Wait, hold on, nine, five, correct. Oh, [sh__. Excuse me.
David Neale [19:35]
People are living in very beautiful homes in San Francisco. You know, voting on very progressive platforms. But in fact, their home was built on the legacy of those trees. You know, but that's, that's what we did, you know.
So now with the Save the Redwoods League, their mission is to preserve the remaining old growth trees that were left. But that mission is largely complete, you know, whatever, old growth trees are left are now more or less protected. So they changed, they're not changed, but transition to a restoration mission, trying to restore stands of trees that were cut over back to their more ancestral state. And that was the justification for bringing in the genome project is to provide them or provide the community, scientists, managers, whatever the modern resource to do that. So that's what we set out to deliver.
With the funding, the scientists could set out and get the genomes of these trees sequenced and then begin to analyze what makes them special.
And here is something you heard at the beginning of this podcast which you might hear differently now that you heard a bit about redwood and about David Neale.
I'm a forester, I've spent my entire career doing genetics of forest trees. I'm a kid who, you know, knew a very, very long time ago, I'd spend his life working on trees.
That was Conversations with scientists. Todays guest was Dr. David Neale, professor emeritus of the University of California Davis.
The music used in this podcast is Break of Dawn by Anthony Vega licensed from artlist.io.
And I just wanted to say because there’s confusion about these things sometimes. University of California Davis and Save the Redwoods League didn't pay for this podcast and nobody paid to be in this podcast.
This is independent journalism that I produce in my living-room. I’m Vivien Marx, thanks for listening.