In 2022, Carla Crossman was analyzing the genes of southern right whales when she came across something unexpected.
Decades earlier, in 1989, researchers had used special crossbows to collect small skin samples from 10 southern right whales in their calving grounds off Argentina’s Valdés Peninsula, as part of an effort to assess the species’ genetic diversity. Crossman, a graduate student at Saint Mary’s University in Halifax, Nova Scotia, was working with those historical samples when she found herself stuck on the DNA results for one whale in particular: Eau10b.
Scientists studying wild animals need a few key numbers to gauge the health of a population. How many individuals are there, for instance? And, of those, how many are female versus male? This sex ratio reveals whether a population is likely to grow.
After sequencing the DNA for each whale, Crossman had quickly scanned the animals’ chromosomes to guess their sexes. With whales, humans, and other mammals—as well as some fish and even plants like ginkgos and kiwis—males have one Y sex chromosome and one X chromosome, while females have two X chromosomes. Crossman’s data showed that Eau10b had two Xs. “I had been fairly confident [Eau10b] was a female,” she says.
Intersex whales swim below the radar, so to speak, because cetaceans have internal genitalia.
But when Crossman checked her guess with a routine sex determination technique, called the SRY test, the answer didn’t make sense.
Scientists use this test to determine whether an animal is carrying the SRY (or “sex-determining region Y”) gene, which helps trigger male development. Because the SRY gene only exists on the Y chromosome, testing for its presence is an easy way to deduce an animal’s sex.
Eau10b’s test showed the SRY gene. The whale was male.
Baffled, Crossman turned to a third technique—a test for a set of genes called ZFX and ZFY that show up on the X and Y chromosomes. In Eau10b, Crossman found both genes, confirming that the animal had a Y chromosome. But the whale’s DNA also contained a double dose of ZFX, the gene carried on the X chromosome. The result revealed that Eau10b had a Y chromosome and two X chromosomes, meaning the animal was neither male nor female. Eau10b was an intersex whale—the first of its species known to scientists.
This combination of sex chromosomes occurs when a cell receives an extra copy of the X chromosome during cell division. A similar event can lead to female offspring with three X chromosomes, or males with one X chromosome and two Y chromosomes.
Crossman doesn’t know how many southern right whales with XXY sex chromosomes might be out there. Even Eau10b’s fate is unknown, since the researchers didn’t identify the whale when they took the DNA sample in 1989. But southern right whales can live up to 70 years, so Eau10b may still be out there touring the globe’s oceans and wintering off the Valdés Peninsula.
While intersex animals are often infertile and unable to produce offspring to help a population grow, Beans Velocci, a historian at the University of Pennsylvania who studies the history of sex classification, says that in social species such as whales, intersex animals likely play important nonreproductive roles that benefit the population in other ways.
Studying intersex animals has helped scientists better understand how genes and hormones shape individuals as they develop. Through the process of domesticating livestock, people have known about intersex cows for thousands of years. On Vanuatu, in the South Pacific, islanders nurture a unique strain of intersex pigs prized for their delicate spiraling tusks. More recently, researchers have also documented intersex horses, dogs, moose, sheep, fish, and many different types of invertebrates. Intersex animals are rare across species, Crossman says, but they’re “more common than we historically thought.”
In humans, the XXY chromosome configuration is called Klinefelter syndrome and occurs in less than 0.1 percent of people—most of whom identify as male and may not even realize they have unusual chromosomes.
The terminology and definitions used to talk about intersex individuals have changed over time, especially when referring to people. But according to Velocci, scientists use the term intersex to describe bodies that, regardless of species, cannot be easily categorized as either male or female.
In social species, intersex animals likely play important nonreproductive roles that benefit the population.
Not all intersex individuals have XXY chromosomes—the term encompasses individuals with a range of characteristics arising from differences in genetics, hormones, and anatomy. An intersex individual may have sex organs or a physical appearance that diverges from the norm. Some individuals, for instance, have a Y chromosome and testes but their cells don’t respond to male sex hormones so their external anatomy is more feminine.
Intersex whales swim below the radar, in particular, because cetaceans have internal genitalia. “You don’t often get a good look at the genitals of a whale,” Crossman says. “Everything is up inside.” Yet scientists have previously found intersex fin whales, belugas, bowhead whales, short-beaked common dolphins, and True’s beaked whales.
“Every time [researchers] are in the field or looking at specimens, they just keep finding these exceptions,” Velocci says. Scientists “have seen over, and over, and over, and over, that sex is clearly not binary.”
But, Velocci says, scientific education has not adapted. “XX and XY are [taught as] the foundation that everything else might deviate from, rather than one possible variation among many.”
For certain well-studied species, such as the endangered North Atlantic right whale—a close relative of the southern right whale—researchers guess an individual’s sex by observing behaviors, such as swimming with a new baby, or obvious external characteristics, like the size and color of the genital slit. But for most whales, DNA tests offer the only answer.
Yet, Eau10b’s story shows that even the most routine sex tests are not perfect. By reducing sex to the presence or absence of a single gene, SRY, scientists risk overlooking animals that don’t fall neatly into a male-female binary. With recent leaps in genetic research, though, it’s now easier to identify intersex animals by comparing results from different tests. “We can just start looking,” Crossman says.
When scientists identify the next intersex animal, that information likely won’t change how its species is managed or understood. But that individual, whether a guppy or a whale, will offer another challenge to rigid definitions of sex. What society deems normal is a box carefully drawn around a wild and messy world, and each individual who can’t be contained offers a fascinating glimpse at nature’s true diversity.
A version of this story originally appeared in bioGraphic, an independent magazine about nature and regeneration powered by the California Academy of Sciences.
Lead image: Tomas Kotouc / Shutterstock
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