Rattlesnake DNA Offers Clues to One of Evolution’s Biggest Mysteries

When most people learn about evolution in school, they’re taught that species are neatly distinct categories. One species becomes two and they can no longer interbreed.

Nature, however, must have skipped that class.

In fact, closely related species like wolves and coyotes often continue exchanging genes long after they begin diverging, and that has left evolutionary biologists wondering exactly how they continue to maintain their unique characteristics.

New research from the lab of Drew Schield, assistant professor of biology at the University of Virginia College and Graduate School of Arts & Sciences, offers insights into the process biologists call the speciation continuum — the gradual, and often messy, process whereby one species slowly loses the ability to interbreed with another.

Published in the journal Proceedings of the National Academy of Sciences, the study analyzed genomes from 181 rattlesnakes representing 12 species across the American West. The work revealed that speciation, or the process by which new species are formed, is not driven by a single “speciation gene,” as some have speculated, but by thousands of genes gradually building barriers to interbreeding over time.

“People often think of species as these very clean, black-and-white categories,” Schield said. “But what we see in nature is that there are often shades of gray. Species can continue exchanging genes while still gradually becoming more distinct.”

Thousands of Small Genetic Differences

The researchers found that early in the speciation process, only a small number of genes may help keep populations distinct. Over time, however, more and more parts of the genome become involved.

Eventually, those many small genetic differences begin working together through genetic associations, forming broader barriers to gene exchange.

“It’s like death by a thousand cuts,” Schield said. “There’s no single gene that explains why these species remain separate. Many genes contribute small effects, and over time those effects become linked together across the genome.”

The study, which drew on more than a decade of fieldwork and relied on the help of researchers across the country, also found that some parts of the genome appear especially important. In particular, the Z chromosome — one of the snakes’ sex chromosomes — showed stronger barriers to gene exchange than the rest of the genome, suggesting sex-linked genes may play an important role in the formation of new species.

The findings help support long-standing evolutionary theories that had been difficult to test in real-world organisms.

“Studies like this are important because they allow us to understand how barriers to gene flow emerge and accumulate across the genome as speciation occurs and ultimately, how biodiversity is generated and maintained,” said Keaka Farleigh, a National Science Foundation postdoctoral research fellow with the Schield Lab and lead author of the paper. 

Why Rattlesnakes?

For Schield, the work also reflects a lifelong fascination with snakes and their biology.

“I’ve always been really inspired by natural systems and by snakes specifically,” he said. “They’re incredible animals. Their variation is such a reflection of the diversity of environments they live in, and they’re a phenomenal system for studying adaptation, evolution and biodiversity.”

His team’s findings may help scientists better understand how new species emerge throughout the natural world, particularly in animals that continue exchanging genes even after diverging. 

According to Schield, the study opens the door to further investigations of how specific genes linked to reproduction, behavior and environmental adaptation contribute to the formation of new species. His team is also interested in combining genomic research with behavioral and ecological studies to better understand how species boundaries are maintained in the wild.

“What really motivates me about this work is that it forces us to rethink simplistic definitions of what a species is,” Schield said. “Nature often doesn’t fit into clean categories, and understanding that complexity is part of what makes evolution so fascinating.”