Farmyards and backyards across Asia are filled to the brim with clucking, strutting chickens by the millions. There, as in much of the world, chickens are found most anywhere people are living. But unlike other areas, the wide swath stretching across Asia from India to southern China and Indonesia is also home to the red junglefowl, the colorful wild pheasant from which the world’s some 33 billion domesticated chickens are descended. And because the two birds sometimes mingle, those ubiquitous domestic chickens may be posing an invisible but serious threat to their wild junglefowl ancestors.
Scientists have discovered that red junglefowl are rapidly losing their genetic diversity and acquiring ever more chicken DNA—up to 50 percent in some birds—through interbreeding with their domestic cousins. The poultry procreation has been rapidly increasing in recent decades, according to a study published Thursday in PLOS Genetics. Loss of diversity is a problem for the wild birds; the more genetically similar to chickens they become, the more susceptible they are to diseases or other dangers posed by a changing environment. And the wild birds are also crucially important for their domesticated descendants. Genetic variations found in wild junglefowl can be used to protect agricultural chickens, by introducing naturally selected genetic diversity that might boost resistance to threats like specific parasites or pathogens. “A loss of wild-type genetic diversity in junglefowl may hinder the safeguarding of one of humanity’s most important food sources,” the authors warn.
Frank Rheindt, of the National University of Singapore, and colleagues studied the genomes of 63 junglefowl found across the bird’s historic natural range from India to China and Indonesia. Most of these samples came from museum specimens that were initially collected more than a century ago, although living birds were included, too. They also described the genomes of 51 domestic chickens in the region. Comparing the genomes from historic and modern junglefowl of all subspecies clearly showed that domestic chicken DNA has become much more common in the wild junglefowl. Today, depending on location, between a fifth and half of the wild junglefowl’s DNA has been inherited from domestic chickens, the authors found.
The historic samples were sourced from the dried toepads of museum specimens at the Lee Kong Chian Natural History Museum of Singapore and the Natural History Museum at Tring in the United Kingdom. They were collected across the wild birds’ natural range between 1874 and 1939, and the authors added an additional 69 samples of both wild and domestic birds from GenBank, a database of publicly available DNA sequences. During the study, the group identified key genetic markers that have dramatically diverged to make domestic birds different from their wild relatives. They found eight key genes that are involved in vision maintenance, sperm fertility, regulating body weight and appetite control.
Chickens are clearly descended from the red junglefowl. But exactly when and where that evolution happened is a matter of long debate. A 2020 genome study suggested that chickens were domesticated in southern China or northern Southeast Asia about 9,500 years ago. Last year, more research resulting in two separate studies concluded that unambiguous domestic chickens first appeared in Thailand only 3,500 years ago, when rice agriculture appeared in areas frequented by the junglefowl. No matter when chickens became truly domestic, some interbreeding between them and wild birds has likely occurred ever since. But the genetic divergence between the two lineages shows that they have largely remained relatively separate—until recent decades. Now, it appears, junglefowl are being domesticated a second time.
Few species have succeeded like the chicken. Junglefowl exist in far more modest numbers, but their populations are robust, and they aren’t currently a threatened species. Yet in recent decades, surging human populations—and their attendant domestic chickens—have steadily encroached on once-wild spaces frequented by the junglefowl. As the two types of birds encounter each other more often, intermixed mating appears to be inevitable.
But Town Peterson, an evolutionary biologist at the University of Kansas, suggests the two species might not actually mate all that frequently. “The behavioral differences between junglefowl and chickens are so massive,” he notes. For several years, Peterson and I. Lehr Brisbin, an ecologist then at the University of Georgia’s Savannah River Ecology Lab, experimented with mixing the two types of birds to see how domestication impacted junglefowl. (At one point two eggs were accidentally switched, so a domestic chicken was hatched in the large pen of junglefowl—and the outlier bird was not hard to identify. “There were 30 skittish birds just flying everywhere, banging into the ceiling and walls, and there was one bird sitting on my boot,” Peterson says.)
“Those crossing events, I bet, are pretty rare,” adds Peterson. “But they do happen, probably where a male junglefowl just takes whatever mate he can get, and it doesn’t have to happen often to erase genetic differences between them.”
Peterson says spotting a hybrid junglefowl by sight is not always easy. He and Brisbin explored interbreeding by studying how the physical evidence of prior influxes of chicken DNA might overwhelm traits of red junglefowl. Historic specimens suggest that some types of plumage that occurred in junglefowl males did begin disappearing decades ago, first in parts of Southeast Asia during the mid-19th century and, by the middle of the 20th century, in Northeast India as well. But further work by Peterson and Brisbin examined whether deliberately interbreeding junglefowl with chickens would change those physical appearances that distinguish the wild birds, like characteristic male plumage or lack of combs in females. The pair found that as they continued to interbreed birds, many of these external signals persisted or even reappeared after further domestic mixing. “The external appearance is very insensitive as an indicator of purity,” Peterson notes. “So this study is really cool, with fascinating insights, and is closer to truth than what we were getting.”
Delving further into historic genetic sampling, Peterson adds, could be a next step to enhance the results—because even the study’s oldest historic samples might not be unambiguously wild junglefowl. By adding more past samples, as well modern birds like the Richardson strain of Indian junglefowl, which is a modern wild lineage in isolation from domestics for decades, could help identify the wildest possible junglefowl genome. “I personally do not think we can pinpoint one location where we are sure to have wild junglefowl, since humans have travelled the globe, bringing with them the chickens, for thousands of years,” adds the study’s first author Meng Yue Wu, who studies population genomics at the National University of Singapore. “We could only choose ‘the most genomically wild’ individuals from our data set.”
Chickens, by far the world’s most populous birds, appear in a colorful diversity of breeds, but over all they are not particularly diverse genetically. The chicken’s genetic homogeneity means that its mixing with wild junglefowl doesn’t add diversity to that species, but instead reduces it. And as wild birds lose genetic adaptations developed over thousands of years, their domestic cousins lose a valuable reservoir of wild genetics that could be used to diversify and strengthen chicken populations. “In [genetically homogenous] populations, diseases spread easily, since there is no standing genetic diversity that may confer resistance,” explains Wu. “Loss of genetic diversity in the wild population may put our domestic stock at risk, [but] preserving wild-type diversity may allow us to introduce relevant adaptations to our domestic stock.”
In the meantime, Peterson warns that the wild birds need protection. “I think that you could make a very strong argument for the [International Union for Conservation of Nature] moving red junglefowl from a species of least concern,” he says, “to one that’s critically endangered, and this study backs that up.”