Mapping the Redwood Genomes

The League leads pioneering research to provide the critical tool in re-establishing logged forests’ genetic diversity and resiliency

Emily Burns, PhD, League's former Director of Science, reaches for the captivating cream-colored needles of an albino sprout growing out of a redwood. “It lacks chlorophyll, so it’s white, and it’s caused by a mutation on that particular sprout’s DNA,” she said. Further genomic research could confirm hypotheses that albino sprouts are more than parasites. It’s clear that the deeper we go into the redwood genome, the more we’ll know. Photo by Paolo Vescia
Emily Burns, PhD, League’s former Director of Science, reaches for the captivating cream-colored needles of an albino sprout growing out of a redwood. “It lacks chlorophyll, so it’s white, and it’s caused by a mutation on that particular sprout’s DNA,” she said. Further genomic research could confirm hypotheses that albino sprouts are more than parasites. It’s clear that the deeper we go into the redwood genome, the more we’ll know. Photo by Paolo Vescia
For anyone new to the San Francisco Bay Area, Redwood Regional Park in the Oakland hills comes as a surprise: 1,830 sylvan acres just minutes from some of the most densely populated real estate in the nation, with 40 miles of trails providing a critical recreational relief valve for diverse urban hikers, runners and equestrians. The park also burgeons with wildlife. A number of charismatic species, including golden eagles, rainbow trout and mountain lions, dwell here. Several distinct biomes are contained within its borders, including mixed coniferous forest, hardwood forest, grasslands and chaparral.

But it is the park’s eponym, the coast redwood, that is both the signature species and the emblem for this property. If you live in San Francisco or the East Bay and you decide to take a quick hike through a redwood forest, this is likely where you’ll come. Still, this isn’t a land of ancient giants, of trees with diameters exceeding 20 feet and heights of more than 300 feet.

While these woods — to paraphrase Robert Frost — are lovely, dark and deep, they’re also young; few redwoods are older than 100 years. While the individual trees are lofty and robust, they’re relatively small when compared to their venerable counterparts in the old-growth groves of the North Coast.
This redwood forest also differs from ancient groves in another way: genetics.

“We know that every decision made on redwood lands over the past 150 years has altered the genetic structure of the forest,” said Emily Burns, PhD, former Director of Science at Save the Redwoods League, during a recent hike in Redwood Regional Park. “Every tree cutting, every replanting project, every restoration thinning — they’ve all selected for specific redwoods and their genes, intentionally or unintentionally.”

And that could be a problem, said Burns. As with all other living things on the planet, genes play a tremendous role in the destiny of redwood trees. Genes can determine if a given tree grows rapidly or slowly; if it can thrive in relatively poor soil or if it requires rich, deep loam; or if it can withstand drought and fight off diseases.

These qualities have particular urgency in the period of climate change that we are now experiencing. Increasingly, scientists refer to this emergent epoch as the Anthropocene — the one superseding the current Holocene, and the first characterized by human impacts.

“There is broad consensus in the scientific community that our climate is changing,” said Burns. “As a whole, our atmosphere and our seas are getting warmer. There are multiple implications to these shifts, and many of them are worrisome. But we don’t have to accept them passively. There’s still much we can do to attempt to slow the process of climate change and ameliorate some of its effects.”

Redwoods and giant sequoia once dominated much of Earth; the great trees were the haunts of the dinosaurs, and after that the mammalian megafauna. But over millions of years, they have been reduced to one isolated area. Coast redwoods now inhabit a narrow littoral strip from just north of the Oregon border to Big Sur, and giant sequoia naturally grow only in 73 groves scattered along the western slope of California’s Sierra Nevada. Since its founding, Save the Redwoods League has been devoted to preserving these remaining stands, protecting them from heavy logging and development.

Restoring the Lost Forests

In recent years, the League’s mandate has expanded to restoration, Burns said. League scientists, volunteers and donors have committed to accelerating old-growth characteristics in young forests by retiring roads, stabilizing soils, selectively thinning overstocked stands, and enhancing riparian woodlands.

“Our research has shown that these restoration treatments create many desired outcomes,” Burns said. “For example, thinning accelerates tree growth rates. However, we don’t yet understand how these and other management practices affect forest genetic diversity. That’s why we’ve launched the Redwood Genome Project with our collaborators, the University of California, Davis, and Johns Hopkins University.”

The project harnesses the latest genomic research methods. Genome sequencing, or determining the order of DNA bases that make up the complete set of genes, has not been possible in conifers until relatively recently. The undertaking will be truly Herculean in the case of coast redwoods because they’re hexaploid: They have six sets of large chromosomes, unlike human beings and giant sequoia, which have two sets (and are hence known as diploid). The coast redwood has a genome 10 times larger than the human genome, and that’s one reason it hasn’t been sequenced. While the giant sequoia genome is smaller, it is still three times the size of the human genome. But it’s essential to sequence both species as soon as possible.

Why? The traits that redwoods and giant sequoia need to weather the rapidly changing climate are expressed through their genes, said Burns. Identifying and protecting forests with diverse genetic traits will help forest managers and conservationists increase the likelihood that the forest will survive and thrive in future conditions.

As the League and its allies move forward with ambitious restoration projects in coming decades, genomic information will be essential in drafting and implementing effective plans.

For example, redwoods are likely to experience significantly more stress in the southern, drier portion of their range than in the northern, wetter portion. So it’s critical that we identify and protect trees that are well adapted to heat and drought — trees that can handle the coming changes.

A forest with limited genetic diversity means it has less chance of adapting to changing environmental conditions. “We need to use this new genetic research to find out where our most genetically diverse forests are and make sure they’re protected,” Burns said.

Creating a Standard: Genetic Conservation

The main work of the $2.6 million Redwood Genome Project will occur over the course of three years, from 2017 through 2019. Ultimately, genetic screening will become a part of standard forest inventory protocols. The goal is to make forest genetic conservation a central element of all forest protection and restoration plans.

Preliminary League-sponsored genetic inquiries already have yielded valuable information about redwood and giant sequoia genetics that will guide the new research, said Burns. By analyzing small sections of DNA called neutral genetic markers, research grantees have discovered that small giant sequoia groves appear to be inbred; that coast redwood “fairy rings” (circles of redwoods around stumps or dead trees) are not always clones; and that the southern giant sequoia population is genetically distinct from the northern population.

“One of our recent grantees, Lakshmi Narayan from the University of California, Berkeley, obtained some stunning data during her doctoral research on coast redwood genetic clones in ancient forests,” said Burns. While scanning redwood trees at Big Basin Redwoods State Park for shared genetic markers, she found that genetic diversity in an old-growth stand was lowest where partial timber harvesting occurred in the past.

That discovery has tremendous implications for conservation forestry generally, and for future redwood and giant sequoia restoration plans specifically. It shows that even minor timber harvests can have profound impacts on the genetics of the forest, potentially affecting forest resiliency decades or centuries into the future. The Redwood Genome Project will expand this groundbreaking research, giving the League and collaborators the genomic tools necessary for the long-term protection of redwoods and giant sequoia.

The Genome Project has specific milestones for its initial three years. In the first year, researchers will develop and publicly release genome sequences for coast redwoods and giant sequoia, using a tree from Butano State Park for the coast redwood genome and a tree from Sequoia National Park for the giant sequoia genome. That will provide baseline sequences for both species.

The second year will be devoted to producing a genetic variation database for the coast redwood and giant sequoia genomes. A variation at a specific site in a DNA sequence is known as a single nucleotide polymorphism, or SNP. A DNA sequence is composed from four nucleotide bases: adenine (A), cytosine (C), guanine (G) and thymine (T). Sometimes there may be a variation in nucleotides at a given known point in a genome. With redwoods, for example, the vast majority of trees may have cytosine at a certain spot in the genome, but a small number of trees may have adenine or guanine. If more than 1 percent of the trees show a variation in a particular point in the DNA sequence, then this variation is considered an SNP.

SNPs may be completely neutral in their impacts, or they may manifest specific effects: susceptibility or resistance to a disease for example, or in the case of redwoods, relative photosynthetic capability, or the ability to withstand specific environmental conditions such as drought.

“By sequencing a diverse panel of trees, we can discover, identify and compare their SNP differences,” said David Neale (external link), a Professor in the Department of Plant Sciences at the University of California, Davis, and a collaborator in the Redwood Genome Project.

Another collaborator in the project, Steven Salzberg (external link), Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science and Biostatistics at Johns Hopkins University, said the hexaploid genome of the coast redwood presents a particular challenge for genomics technology. “But our recent experience sequencing the very large genomes of three other conifer species gives us confidence that we’re ready to take on the redwood,” Salzberg said.

Once the data are analyzed, they will be used to create “SNP chips,” genotyping tools that contain tens of thousands of genetic variations. Leaves will be collected in the field and taken to a lab for analysis with the SNP chips to rapidly and cost-effectively assess individual trees.

“We’ll release the SNP chip designs to the public so other researchers can use them in their own coast redwood and giant sequoia studies,” said Neale. “Their work will augment our work, and vice versa.”

During the third year, researchers will conduct genomic studies on a broad scale, using SNP chips to sample hundreds of coast redwoods and giant sequoia.

“This initial survey will allow us to refine our techniques, pointing the way for other research groups to expand our genomic knowledge base for coast redwoods and giant sequoia,” Burns said. “We anticipate that we’ll be conducting genetic assessments on a wide scale once we’ve fully deployed the genomic tools we’re developing.”

Using the genomic tools, restoration field teams will be able to tell the difference between planted clones and native trees. Then they can select clones to remove to restore the stand’s natural diversity and resiliency.

A Captivating Mutation

During her hike in Redwood Regional Park, Burns pointed out something anomalous in the forest — a cream-colored albino redwood sprig that stood out starkly against the surrounding dark green foliage.

“It can’t photosynthesize by itself, so it’s subsidized by sugars contributed from the tree’s unaffected foliage,” she said.

Albinism in redwoods occurs more in the southern portion of the range than the northern, and there’s some evidence that albino sprouts may accumulate heavy metals for the general benefit of the tree. They may be something more than parasites, and further genomic research could reveal the answer. It’s clear that the deeper we go into the redwood genome, the more we’ll know. And in conservation science — as with most things — knowledge is power.

Learn More

See a timeline of the Redwood Genome Project.

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About Glen Martin

Avatar for Glen Martin

Glen Martin was an environmental reporter for the San Francisco Chronicle for many years, and has contributed to more than 50 magazines, including Discover, Audubon, Men’s Journal, Forbes, Sierra, Outside, Recode and Wired. Before his journalism career, Martin worked as a wildfire fighter for the U.S. Forest Service in the Shasta/Trinity and Mount Baker National Forests. His book, Game Changer: Animal Rights and the Fate of Africa’s Wildlife, was published in 2012 by the University of California Press.

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4 Responses to “Mapping the Redwood Genomes”

  1. Mohsin Noor

    Amazing post, thank you for sharing this knowledge to us. This is very interesting.

  2. james

    Redwoods League has protected nearly all of the ancient redwood groves that exist on the planet following 150 years of wide-scale logging across the natural range of the redwood forest.

  3. jerome

    I agree! A hundred years ago the great original Redwood forest covered two million acres along the California coast.

  4. BD

    Absolutely! They grow within a mile of each other on Redwood Creek along the northern California coast.


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