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When scientists want to trace how a species has changed over time—and predict its prospects for survival—they turn to DNA. But what if the genetic map guiding them belongs to the wrong animal?

A study led by researchers at the USC Dornsife College of Letters, Arts and Sciences shows that using the wrong "reference genome"—the master sequence scientists rely on to compare DNA—can significantly distort the picture. For the gray fox, one of North America's most common wild canids, mapping against a dog or Arctic fox genome, instead of its own, made populations look smaller, less diverse and even in decline when they were actually stable or growing.

"It turns out the reference you use really changes the story you tell about a species," said Jazlyn Mooney, Gabilan Assistant Professor of Quantitative and Computational Biology at USC Dornsife and corresponding author of the study in Cell. "If you use the wrong reference, you can end up with misleading answers about a species's history or health, and even its chances of long-term survival."

Scientists put a reference genome to the test

Every genetic study needs a starting point: a reference genome, usually built by sequencing the DNA of one individual of a species. When scientists study additional individuals, they align the new DNA against that reference for comparison.

But many species, especially those less studied, lack their own reference. In these cases, researchers turn to the next best option—a close relative. For decades, the domestic dog's genome has stood in for foxes, wolves and wild dogs.

Mooney and her colleagues wondered just how much that choice mattered. Would using a genetically distant blueprint simply blur the details, or could it actually rewrite the story?

The team re-analyzed DNA from 12 gray foxes—six from eastern North America and six from the West—comparing how their genomes aligned to three different references: the gray fox itself, the domestic dog and the Arctic fox.

They asked:

• How much genetic variation appears?
• What does the data reveal about past population sizes?
• Are current populations growing or shrinking?
• Which genes seem to be under natural selection, hinting at adaptation?

The answers depended heavily on which genome served as the map.

With the gray fox's own genome, researchers detected 26%–32% more genetic differences among individuals and about a third more rare variants (the subtle DNA changes that reveal how populations have been evolving recently).

Estimates of population size were also 30%–60% higher. In the western United States, for instance, the gray fox genome showed stability and growth, while the dog and Arctic fox genomes suggested decline.

The wrong reference also threw off measures of how DNA shuffles during reproduction. With the dog or Arctic fox genomes, the numbers sometimes doubled or even tripled compared with the gray fox genome, especially near the ends of chromosomes.

"This is the kind of thing that could change conservation decisions," Mooney said. "If you think a population is shrinking when it's not, or vice versa, you might end up protecting the wrong group or missing an opportunity to safeguard genetic diversity."

The study also showed that using the wrong reference could create misleading signs of natural selection. The dog and Arctic fox genomes identified twice as many potential DNA "hot spots"— regions that looked like they might be adaptive—compared with the gray fox genome. Many of these signals were false alarms, caused by the mismatch between species.

Why the right reference genome matters for conservation and people

The study's implications go well beyond foxes. Conservation biologists use genetic data to decide which populations to protect, how to design breeding programs and whether endangered species are at risk of inbreeding. If the genetic picture is distorted, those decisions may rest on shaky ground.

That could affect high-profile species such as the Ethiopian wolf, the African wild dog or even the tiny Channel Island foxes off Southern California's coast. For animals already on the edge, a flawed map could mean misjudging their vulnerability.

"Maintaining the world's biodiversity isn't just about saving animals for their own sake," Mooney said. "Biodiversity supports clean water, food security and climate stability. If conservation plans are based on incomplete or biased genetic information, we risk mismanaging species and weakening the natural systems people depend on."

These findings echo a lesson from human genetics: For years, the human reference genome drew mostly from just a few people, limiting research across populations. More recent efforts are building references that better reflect global diversity.

Scientists call for better genomic maps

The researchers argue that the solution is to invest in building species-specific reference genomes. Assembling a high-quality genome sequence is expensive, and nearly 99% of species still lack one, but the payoff could be crucial.

For species without their own reference, Mooney and her team point to new computational methods and building high-quality genomes that capture more of a species's diversity—as ways to reduce bias.

"We're not saying every species will be as impacted as gray foxes," Mooney said. "But our study shows the risks are real, and can lead you astray."

The gray fox study stands as both a warning and a call to action: Choosing the wrong reference doesn't just blur the details—it can redraw a species's past and future.