Extracting new science from ancient pollen

DNA, isotopes from red spruce helping researchers measure trees' response to climate change over time

Embedded in the mud at the bottom of lakes is a natural time capsule, preserved over centuries and millennia.

Scientists have long used fossil pollen to understand how forests have changed since the last ice age, and now, new advances in science and technology can reveal even more.

A team of scientists from the University of Maryland Center for Environmental Science are working to find and sequence DNA held within the ancient pollen of trees and compare it with what they find in the same species rooted on today’s landscape. By examining genes and isotopes held within these trees from the past and present, the scientists can draw better conclusions about how trees may respond to ongoing and future climate changes.

“The problem with trying to understand how species respond to climate change is that responses for forests take place over decades or centuries. It’s not like we can just go out and watch and see what happens,” said Matt Fitzpatrick, an associate professor at UMCES’ Appalachian Laboratory. “We have to come up with ways we can get some data on responses. One way of doing that is looking at how they’ve responded to climate change in the past.”

Advances in the field will help clarify some long-standing questions for Fitzpatrick and his team, which includes Appalachian Laboratory’s David Nelson and Cat Stylinski. It has only become possible in recent years for scientists to sequence DNA from ancient pollen. Coupled with instruments in Nelson’s lab that can measure the isotopic makeup of a sample as minuscule as pollen, the team can learn about the physiology of trees that were alive thousands of years ago.

The three-year study will focus on red spruce trees. Because of its abundance and tendency to produce a lot of pollen, the team has a higher likelihood of finding its pollen in ancient mud at the bottom of lakes.

Red spruce also has a unique distribution, said Nelson, an associate professor at Appalachian Laboratory. Large populations of red spruce live in New England. The species continue south through Maryland where it was once abundant, but now lives in isolated cold, damp pockets found on mountain tops.

“We’re hoping that some of the things we learn from this particular species can inform our understanding of how other tree species will or won’t adapt or respond to climate change,” Nelson said.

You could use Maryland as an example. If you go back 20,000 years, the pollen shows the plants that were here are very much like what you’d find in Canada and Alaska today.

Matt Fitzpatrick
Associate professor, Appalachian Laboratory

Uncovering fossil pollen

Thousands of years ago, just like it does now, some tree pollen fell back to earth’s surface. Pollen grains landing on lakes eventually sunk and became preserved in new layers of sediment.

Scientists can core these lake bottoms to uncover a muddy timeline dating back thousands of years. The deeper their core, the older the pollen they recover.

In addition to looking for pollen, they scour these samples to find pieces of plants using isotopes. Using a common practice of carbon dating, they can use the plant material to estimate ages for the pollen they find: Plants stop taking in carbon dioxide when they die, and one form, carbon-14, will decay through time. The amount of carbon 14 in a plant sample helps scientists estimate the age of the sediments.

Nelson also will be using stable forms of carbon, 12 and 13, to determine how much heat and drought stressed red spruce trees in different locations at different points in time.

Plants take in carbon molecules as carbon dioxide during photosynthesis and they prefer CO2 with carbon-12. Plants can be picky and reject carbon dioxide molecules with carbon-13, but only if they have access to enough water and other resources. When plants lack enough water, they will take whatever they can get, which means they will take up more carbon dioxide molecules containing carbon-13.

The carbon makeup that Nelson measures in the pollen offers clues of whether it was thriving or suffering in its environment.

Like birds, plants can migrate in response to temperature change, though the process takes centuries instead of months. By producing seeds, a tree can march toward a newer home by a few meters each year.

“You could use Maryland as an example,” Fitzpatrick said. “If you go back 20,000 years, the pollen shows the plants that were here are very much like what you’d find in Canada and Alaska today.”

What a plant’s isotopes indicate can be combined with what the team learns from the pollen’s DNA to reveal more about red spruce’s population changes. There are limits, however.

In ancient pollen, the DNA can be degraded, limiting what scientists can read just like trying to read a page of a book put through a shredder. It’s difficult to understand the whole story.

Even partly degraded DNA, however, can indicate gene flow between populations. That’s enough to help scientists determine if its tree was part of a small or large population, and even whether the population was growing or shrinking.

“Imagine human populations that have been isolated for a very long time: we look different, we don’t have direct relatives in these different populations,” Fitzpatrick said. “The closer we are to one another, the more likely we are to exchange genes and the more closely related we’ll be.”

Those details are key to broadening scientific understanding of tree migration, including when in a millennia-long timeline red spruce started disappearing from some places and burgeoning in others.

Measuring climate response

Scientists can give more context to their findings from the past when they start sequencing DNA from modern-day trees, which tell a complete story.

Like having two copies of the same book, the scientists can look at the DNA of trees across the same species and identify typos—or in the case of genes, single nucleotide polymorphisms, which provide a signal of a species’ ability to adapt to its environment.

“With those, we are going to be able to make inferences. If these are the traits that drive climate adaptation in red spruce, do we see populations with those traits in the past doing well or doing poorly?” Fitzpatrick said. “We can’t say they were adapted to climate or not, but we can say something about how they were responding to climate change and see if that is consistent with the traits we think those populations had.”

Work on the project started in summer 2017 with sample collection. The scientists and their collaborators collected seeds and needles on living red spruce scattered along the eastern United States from northern New England to the Appalachians Mountains in North Carolina.

Needles were easy to gather as the scientists clipped them from trees before bottling them in small tubes. The cones containing some of the seeds required more creativity. Using a slingshot attached to a long standing pole, the scientists took turns aiming at the tallest tree tops, vying to topple some cones.

The needles can be used to study that tree’s DNA and isotopes. Using their lessons from studying the genes and isotopes, the scientists can build models that forecast a possible future of the species based on their lessons from the past.

The seeds they collected come from roughly 400 individual trees across the New England to North Carolina range. Each will be planted in common gardens along the same range: one at Appalachian Laboratory in Frostburg, another at the University of Vermont, and one at a U.S. Forest Service site in North Carolina. Then they can monitor the spruces’ ability to thrive in the given environment as another lesson in a species’ ability to adapt to climate stress.

“We’re curious about how well we can predict the changes we observe from our collections of fossil pollen and the spatial variability we see in current populations,” Fitzpatrick said. “How well can we use that information to predict responses to climate change?”