Research Magazine 2009
A diagram representing the divergence of species, from the first edition of Charles Darwin’s On the Origin of Species (1859).
Image from Wikimedia Commons
Rightly or wrongly, the greatest contributions to knowledge are often boiled down to a single word. Thomas Edison: lightbulb. Marie Skłodowska-Curie: radioactivity. Albert Einstein: relativity. Charles Darwin: evolution. But, in fact, Darwin wasn’t the first to propose a theory of evolution, he was first to explain how evolution works, through the mechanism of natural selection.
A century and a half after Darwin published his ideas, scientists are continuing to expand our understanding of how and why natural selection occurs. At BU, biochemists are revealing the importance of DNA’s shape in genetic expression and mutation, while biologists are studying the genes of sea anemones and the behavior of treefrogs to explain the history of evolutionary change. And this year—the 200th anniversary of Darwin’s birth and 150th anniversary of his On the Origin of Species—scientists here are joining with colleagues throughout the University, from chefs in the Gastronomy Program to actors in the School of Theatre, in a yearlong celebration of Darwin’s life and work.
Shape Counts in DNA’s Code
A chromosome progressively unfolds as chromatin, the 30-nanometer filament, nucleosomes, the DNA double helix, and finally the letters representing the nucleotide sequence.
Image courtesy of Tom Tullius
The double helix of DNA—the elegant simplicity of four base pairs connected in long, twisting strands that write the genetic instructions for all life—is what Francis Crick and James Watson discovered in 1953.
They didn’t know the half of it.
A collaboration of Boston University and National Institutes of Health (NIH) scientists has found that the shape of DNA—the molecule’s width and its nooks and crannies—may be as important as the base-pair sequences in translating genetic codes into living organisms. Their findings, which appeared in the March 12, 2009, online edition of Science, could revolutionize genomics and help unravel the genetic underpinnings of disease.
“DNA is not a perfectly uniform double helix,” says Chemistry Professor Tom Tullius, who collaborated on the research with bioinformatics doctoral students Stephen Parker and Loren Hansen, along with researchers at NIH’s National Human Genome Research Institute (NHGRI) led by NHGRI investigator Elliott Margulies. “There are subtle differences in the shape of the molecule that are very important to the binding of proteins.” These proteins, known as transcription factors, allow DNA to produce yet more proteins and also to regulate when, where, and how many of these vital compounds are created.
Tullius and his fellow researchers compared a well-studied 1 percent of the human genome (30 million base pairs of DNA) to corresponding segments of DNA from 36 mammals, including mice, chimpanzees, and rabbits. They were looking for overlaps, believing that if a portion of the genome is the same across many species, it must be important.
“Mutations occur randomly,” explains Parker. “But they’re rejected in functionally important areas”—meaning that genetic mutations that alter vital functions won’t be passed on because organisms with those mutations won’t survive to reproduce. The genetic coding for these important functions is said to be “conserved” or “constrained” by evolution.
A few years ago, other researchers did a similar cross-species comparison and found that about 6 percent of the genome section they studied was constrained by evolution. But that study looked only at base pairs. The BU researchers incorporated the shape of each sequence in their comparison, using an algorithm developed by Parker. When shape was taken into account, the percentage of the genome that appeared to be constrained doubled.
According to Tullius, this indicates that a lot of DNA’s function may be determined by the molecule’s shape, even if a few base pairs have been shuffled across many generations.
“DNA is not a perfectly uniform double helix. There are subtle differences in the shape of the molecule.”
The researchers also found that DNA shape alters much more as a result of genetic mutations known to cause disease or biological change versus mutations that aren’t known to impact any biological function.
“What that means is that larger structural changes correspond to biological consequences,” says Parker.
This could impact the booming field of research on associations between genetic mutations and disease. Only a fraction of mutations known to impact biological function exist among the 2 percent of the human genome that directly codes for proteins. The vast majority of them, including more than 700 mutations studied by the BU team, exist among the remaining 98 percent of base pairs, whose role is understood less well.
“They’re out there in terra incognita,” says Tullius, “where you have a very hard time figuring out what went wrong and why this particular change led to heart disease or dementia.” A focus on DNA shape offers a new way to interpret these mutations.
The next step will be to expand this analysis to the entire genome, creating a topographical DNA map that includes identification of biologically important regions through comparisons with other mammals, transcription proteins that bind to different DNA shapes, and mutations that affect those structures.
“There’s all this stuff that’s invisible to us now,” says Tullius, “but we’re getting a clue about what’s happening out there.”
Our Anemone Ancestor
Could a tiny sea anemone from the salt marshes of New England reveal some of the secrets of evolution? Associate Professor of Biology John Finnerty thinks so. His lab has become internationally known as a center of research into an important new model animal for evolutionary study, the Nematostella vectensis, or starlet sea anemone—an elegant name for a wisp of a creature the size of a grain of rice. In the lab and in its native estuaries, Nematostella offers a fresh angle on the evolutionary development of humans and on the effects of climate change.
Finnerty’s team attempts to explain biodiversity by comparing animal genomes and pinpointing areas of “novelty and innovation”—points at which one genome is not like another. In seeking to understand what makes humans human, for example, the researchers look at the genomes of simpler creatures and try to identify the variations that ultimately led to human complexity.
Biologists have generally assumed that “there were going to be lots of innovations in the human genome that make us complex,” says Finnerty. “The first animal genomes we compared ourselves with were Drosophila [the fruit fly] and nematode [the roundworm]. Certain genes were present in us and absent in them, and so the assumption was that these might be some of the inventions that helped make us who we are.”
The fruit fly and the worm, two of the most common model organisms in biology, provide a glimpse back in genetic time to an early stage in animal evolution, Finnerty says, but the sea anemone “takes us to an even earlier point in time.” It shares 80 percent of our genes, including “some really interesting animal-specific traits,” like nerve cells, muscle cells, and even signs of a bilateral body plan, as Finnerty first reported in Science in 2004, something long thought to be the exclusive domain of so-called higher animals.
The genome of the starlet sea anemone, Nematostella vectensis, has a surprising amount in common with that of humans, including a representative of one of the genes involved in breast cancer. Here, an adult female floats next to a mass of eggs while a ”two-headed“ anemone undergoes a form of asexual reproduction.
Photo courtesy of Adam Reitzel
“Some of the things that we thought were human inventions, because they were missing in the fruit fly and the nematode, were actually present in Nematostella,” says Finnerty. “That suggests that not only are those genes not human inventions, but that they trace their legacy way back in animal evolution—that the basic animal blueprint may be very, very old.”
In a recent article in the journal Genome, Finnerty and his former doctoral student James Sullivan report that an unexpectedly high proportion of human disease genes are present in this simple animal. “It turns out, for example, that there’s a really good representative in Nematostella of one of the genes involved in breast cancer,” Finnerty says. “That just blows people’s minds, because that’s a very mammalian disease. But this is a gene that has an ancient history, and sometimes understanding the history can help inform the medical studies. You can look at how the gene evolved over hundreds of millions of years and say, that particular change really stands out, and let’s investigate whether that might be important.”
It’s not only the ancient lineage of the animal that holds Finnerty’s interest. He’s looking now at finer-scale genetic variations within Nematostella populations, measuring how different groups react to environmental stresses. “Nematostella live in estuaries, which are really in the crosshairs of a lot of the impacts we make on the planet. These guys are like the canary in the coal mine,” he says.
With his students, he’s comparing these sea anemones from South Carolina, New Jersey, Massachusetts, and Nova Scotia, finding that “some can grow faster at higher temperatures, or they can regenerate faster at higher temperatures, and that’s of course very relevant for climate change.”
“We think these guys live under the mantra ‘adapt or die,’” Finnerty says. “They can’t really move north with increasing temperatures, as we believe some species are doing, like the maples in Vermont. We think it’s a great model to understand how other animals might adapt.”
Flexible Frog—An Evolutionary Find
Photo courtesy of Justin Touchon
You might call it the curious incident of the frogs in the night.
At two tropical ponds in Panama a few years ago, biologist Justin Touchon—then a BU graduate student, now a postdoctoral research fellow—was researching the eggs and tadpoles of the hourglass treefrog (Dendropsophus ebraccatus), known to lay its eggs terrestrially, on vegetation above water. A third pond nearby was filled with the same species, but the plants over it lacked any visible egg clutches. Intrigued by the absence of eggs at the third pond, Touchon and Karen Warkentin, a biology associate professor, staked out the pond one night and were amazed to see frogs laying eggs in the water, on submerged vegetation.
Until that moment, all 5,000 or so frog species were thought to lay either aquatic eggs—which are susceptible to drying out if stranded out of water—or terrestrial eggs, vulnerable to drowning if submerged. None was believed to do both.
Warkentin was fascinated by their find and urged Touchon to conduct further research. The possible implications for our understanding of evolution, she says, are what make this discovery so intriguing.
Laying eggs on land is an evolutionarily derived behavior: the ancestors of all modern frogs laid eggs exclusively in water (as most still do), but at various times long ago, evolutionary pressures led some frogs to start laying their eggs on land, forming new branches on the frog family tree. Studying a frog species that displays both egg-laying behaviors, says Warkentin, could provide insights into how and why the evolutionary change from aquatic to terrestrial reproduction took place.
“It will be shocking to me if Dendropsophus ebraccatus is the only frog that does this, because nature just doesn’t work that way.”
But before they could consider these larger evolutionary questions, Warkentin and Touchon first had to verify that the hourglass species truly could lay eggs both on land and in water. Because the two ponds where Touchon’s initial research was based were shaded by a thick forest canopy and the third pond was much more exposed, the researchers tested whether this environmental cue was driving the frogs’ egg-laying behavior. They created a dozen mini–pond habitats using plastic kiddie pools, placing half of the pools in the forest and half in a nearby open field. Over a series of nights, they put a single pair of breeding frogs into each pool, choosing frogs from all three ponds and covering the habitats with a cage to ensure that each breeding pair had exclusive use of the area.
Indeed, as reported in the May 27, 2008 issue of the Proceedings of the National Academy of Sciences, the frogs deposited the majority of their eggs in water when in the exposed habitats and the majority of their eggs on land in the more shaded habitats. It didn’t matter which of the three natural ponds the frogs originally came from, says Touchon. “Even frogs from ponds where we’d never seen eggs in the water laid eggs aquatically when placed in the sunnier areas,” he says.
The eggs appear to survive both on land and in water by not being extremely well suited for either environment: hourglass treefrog eggs deposited on land need rain to survive; eggs deposited in water drown if they’re too far from the water’s surface.
Touchon’s more recent experiments testing frogs’ reactions to aquatic predators have produced similarly interesting results. “It definitely appears that the frogs can detect cues from predators in the water, in addition to variation in the canopy,” he says. “So they’re really able to assess, in a very fine-tuned manner, the quality of the habitat for their eggs.”
Biologist Karen Warkentin and postdoctoral fellow Justin Touchon in the field in Panama, where they discovered that the hourglass treefrog is capable of laying eggs on land and in water—a previously unknown example of plasticity that could shed light on the evolutionary transition from aquatic to terrestrial egg-laying in other frog species.
Photos courtesy of Justin Touchon
This discovery of behavioral flexibility in laying eggs on land or in water, says Warkentin, may add to our understanding of how evolution takes place. Some scientists, she says, believe phenotypic plasticity—the ability of an organism to change its traits or behaviors in response to its environment—plays an important role in evolution, but without being able to travel back in time to watch evolution unfold, they’ve had difficulty testing this hypothesis. Discovering plasticity in a contemporary species creates opportunities both for experimental work to test how natural selection acts on egg-laying sites and for comparative research to assess the role of plasticity in the evolutionary transition to laying eggs on land.
And Warkentin suspects they’ll find more frog species that display such plasticity, providing additional evidence. “It will be shocking to me if Dendropsophus ebraccatus is the only frog that does this, because nature just doesn’t work that way,” she says, explaining that scientists likely haven’t noticed this plasticity before because they haven’t been looking for it. “This could be an example of how thinking you know the answer can blind you to something that’s right under your nose.”
Touchon and Warkentin’s discovery may also help answer questions about why this particular evolutionary change—the transition from aquatic to terrestrial reproduction—occurred. Researchers have many ideas about what evolutionary pressures led to the change; finding a frog that can deposit eggs on land and in water, Touchon and Warkentin say, allows them to manipulate the environment and—for the very first time—experimentally test hypotheses about these pressures.
Students in the College of Fine Arts took a non-realistic approach to their production of Peter Parnell’s Trumpery, which explores the tensions and apprehensions behind Darwin’s long wait to publish his theory of natural selection.
Charles Darwin began formulating his theory of evolution by natural selection in the 1830s but didn’t publish his first paper on the topic until 1858—more than 20 years later. Darwin’s biographers propose widely varying explanations for this two-decade gap. Some paint Darwin as a careful collector of facts, who patiently waited to publish until he’d gathered sufficient evidence for his theory. Others describe years of hesitation and handwringing as Darwin stewed over the possible social and religious ramifications of publishing his ideas.
The latter interpretation provides the basis for Trumpery, a drama by American playwright Peter Parnell. School of Theatre Director Jim Petosa and an all-student cast and crew brought the play to the Boston University Theatre in May 2009 as their contribution to the Greater Boston Darwin Bicentennial celebration.
Trumpery depicts Darwin’s reluctant race to secure his legacy as the father of natural selection by completing and publishing On the Origin of Species before a young British biologist, Alfred Russel Wallace, can trump him by publishing his own similar ideas. In the play, the quest nearly shatters Darwin: “If I finish, I’m a killer,” his character says. “I murder God.”
While more fiction than fact, the play succeeds in revealing, in Petosa’s words, “human truths,” and audiences at the BU Theatre were riveted by its exploration of the tensions between science and faith—as compelling now as they were in Darwin’s day.